Repository: marrink-lab/vermouth-martinize (language: python)

Issue:
rename elnedyn to elnedyn21
Currently the elnedyn force-field which is based on protein force-field 21 is just named elnedyn. For book-keeping purposes changing to elnedyn21 was suggested by Paulo
Fix/425
This PR fixes issues #425 and #426 and #427. 


Discussion / hints:

Fix patch:
diff --git a/doc/source/conf.py b/doc/source/conf.py
index 88219c8d4..318342a0c 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -71,7 +71,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
diff --git a/vermouth/data/force_fields/elnedyn/aminoacids.ff b/vermouth/data/force_fields/elnedyn21/aminoacids.ff
similarity index 99%
rename from vermouth/data/force_fields/elnedyn/aminoacids.ff
rename to vermouth/data/force_fields/elnedyn21/aminoacids.ff
index b76ad220a..fd25a19fa 100644
--- a/vermouth/data/force_fields/elnedyn/aminoacids.ff
+++ b/vermouth/data/force_fields/elnedyn21/aminoacids.ff
@@ -140,7 +140,7 @@ PRO                1
 [ atoms ]
 ;id type resnr residu atom cgnr   charge
  1   Na   1     PRO     BB     1      0    
- 2   C2   1     PRO     SC1    2      0    
+ 2  AC2   1     PRO     SC1    2      0    
 
 [constraints]
 #meta {"group": "Side chain bonds"}
diff --git a/vermouth/data/force_fields/elnedyn/citations.bib b/vermouth/data/force_fields/elnedyn21/citations.bib
similarity index 100%
rename from vermouth/data/force_fields/elnedyn/citations.bib
rename to vermouth/data/force_fields/elnedyn21/citations.bib
diff --git a/vermouth/data/force_fields/elnedyn/general.ff b/vermouth/data/force_fields/elnedyn21/general.ff
similarity index 100%
rename from vermouth/data/force_fields/elnedyn/general.ff
rename to vermouth/data/force_fields/elnedyn21/general.ff
diff --git a/vermouth/data/force_fields/elnedyn/modifications.ff b/vermouth/data/force_fields/elnedyn21/modifications.ff
similarity index 100%
rename from vermouth/data/force_fields/elnedyn/modifications.ff
rename to vermouth/data/force_fields/elnedyn21/modifications.ff
diff --git a/vermouth/data/force_fields/elnedyn22p/aminoacids.ff b/vermouth/data/force_fields/elnedyn22p/aminoacids.ff
index 894de0947..6dfb9ef52 100644
--- a/vermouth/data/force_fields/elnedyn22p/aminoacids.ff
+++ b/vermouth/data/force_fields/elnedyn22p/aminoacids.ff
@@ -75,7 +75,7 @@ VAL                1
 [ atoms ]
 ;id type resnr residu atom cgnr   charge
  1   P5   1     VAL     BB     1      0    
- 2   AC2  1     VAL     SC1    2      0    
+ 2   C2  1     VAL     SC1    2      0    
 
 [constraints]
 ;  i     j   funct   length  
@@ -91,7 +91,7 @@ LEU                1
 [ atoms ]
 ;id type resnr residu atom cgnr   charge
  1   P5   1     LEU     BB     1      0    
- 2   AC1  1     LEU     SC1    2      0    
+ 2   C1  1     LEU     SC1    2      0    
 
 [constraints]
 #meta {"group": "Side chain bonds"}
@@ -108,7 +108,7 @@ ILE                1
 [ atoms ]
 ;id type resnr residu atom cgnr   charge
  1   P5   1     ILE     BB     1      0    
- 2   AC1  1     ILE     SC1    2      0    
+ 2   C1  1     ILE     SC1    2      0    
 
 [bonds]
 #meta {"group": "Side chain bonds"}
@@ -159,13 +159,26 @@ ASN                1
 [ atoms ]
 ;id type resnr residu atom cgnr   charge
  1   P5    1     ASN     BB     1      0    
- 2   P5    1     ASN     SC1    2      0    
+ 2   Nda   1     ASN     SC1    2      0    
+ 3   D     1     ASN     SCP    3  +0.46  36 {"charge_dummy": 0.14}
+ 4   D     1     ASN     SCN    4  -0.46  36 {"charge_dummy": 0.14}
+
+[virtual_sites2]
+; Site from       funct a
+   2     3    4   1     0.5
+
+[ edges ]
+SCP SC1
+SCN SC1
 
 [ constraints ]
 #meta {"group": "Side chain bonds"}
 ;  i     j   funct   length
    1     2    1       0.250
 
+[constraints]
+;  i     j   funct   length
+   3     4    1       0.28
 
 ;;; GLUTAMINE
 
@@ -280,7 +293,7 @@ THR                1
 [ atoms ]
 ;id type resnr residu atom cgnr   charge
 1   P5     1     THR     BB     1      0    
-2   P1     1     THR     SC1    2      0     0
+2   N0     1     THR     SC1    2      0     0
 3   D      1     THR     SCP    3  +0.36    36 {"charge_dummy": 0.14}
 4   D      1     THR     SCN    4  -0.36    36 {"charge_dummy": 0.14}
 
diff --git a/vermouth/data/mappings/elnedyn/ala.charmm36.map b/vermouth/data/mappings/elnedyn/ala.charmm36.map
old mode 100755
new mode 100644
index 240455ba2..b65dbc71b
--- a/vermouth/data/mappings/elnedyn/ala.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/ala.charmm36.map
@@ -19,7 +19,7 @@ ALA
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 elnedyn22p
 
diff --git a/vermouth/data/mappings/elnedyn/arg.charmm36.map b/vermouth/data/mappings/elnedyn/arg.charmm36.map
index a8db26900..aaa99ffad 100644
--- a/vermouth/data/mappings/elnedyn/arg.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/arg.charmm36.map
@@ -19,7 +19,7 @@ ARG
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 
 [ martini ]
diff --git a/vermouth/data/mappings/elnedyn/asn.charmm36.map b/vermouth/data/mappings/elnedyn/asn.charmm36.map
old mode 100755
new mode 100644
index 5b1003cdd..dad8d4f45
--- a/vermouth/data/mappings/elnedyn/asn.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/asn.charmm36.map
@@ -19,7 +19,7 @@ ASN
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 
 [ martini ]
diff --git a/vermouth/data/mappings/elnedyn/asp.charmm36.map b/vermouth/data/mappings/elnedyn/asp.charmm36.map
old mode 100755
new mode 100644
index 2469fc99e..19aab52aa
--- a/vermouth/data/mappings/elnedyn/asp.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/asp.charmm36.map
@@ -19,7 +19,7 @@ ASP
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 
 [ martini ]
diff --git a/vermouth/data/mappings/elnedyn/chol.charmm36.map b/vermouth/data/mappings/elnedyn/chol.charmm36.map
deleted file mode 100644
index 664f3bc2e..000000000
--- a/vermouth/data/mappings/elnedyn/chol.charmm36.map
+++ /dev/null
@@ -1,141 +0,0 @@
-; Copyright 2018 University of Groningen
-;
-; Licensed under the Apache License, Version 2.0 (the "License");
-; you may not use this file except in compliance with the License.
-; You may obtain a copy of the License at
-;
-;    http://www.apache.org/licenses/LICENSE-2.0
-;
-; Unless required by applicable law or agreed to in writing, software
-; distributed under the License is distributed on an "AS IS" BASIS,
-; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-; See the License for the specific language governing permissions and
-; limitations under the License.
-
-[ molecule ]
-CHOL
-
-[from]
-universal
-
-[to]
-elnedyn
-elnedyn22
-elnedyn22p
-
-[ martini ]
-ROH R1 R2 R3 R4 R5 C1 C2
-
-[ mapping ]
-charmm27 charmm36
-
-[ atoms ]
-    1    C1   ROH ROH ROH R1
-    2    O2   ROH
-    3    H3   ROH
-    4    H4   ROH 
-    5    C5   ROH ROH ROH R2
-    6    H6   ROH ROH ROH R2
-    7    H7   ROH ROH ROH R2
-    8    C8    R1 ROH ROH R2 R2
-    9    C9    R2 R2 R2 R2 ROH
-   10   H10    R2 R2 R2 R2 ROH
-   11   C11    R2
-   12   H12    R2
-   13   H13    R2
-   14   C14    R2 R2 R3 R4
-   15   H15    R2 R2 R3 R4
-   16   C16    R4 R4 R3
-   17   H17    R4
-   18   C18    R4
-   19   H19    R4
-   20   H20    R4
-   21   C21    R4 R4 C1
-   22   H22    R4 R4 C1
-   23   H23    R4 R4 C1
-   24   C24    R5 R4 C1 C1
-   25   H25    R5 R3 R4 C1 C1
-   26   C26    R5 
-   27   C27    R5
-   28   H28    R5
-   29   H29    R5
-   30   H30    R5
-   31   C31    R3 R3 R3 C1
-   32   H32    R3 R3 R3 C1
-   33   H33    R3 R3 R3 C1
-   34   C34    R3 
-   35   H35    R3
-   36   H36    R3
-   37   C37    R3 R3 R3 R2 ROH
-   38   H38    R3 R3 R3 R2 ROH
-   39   C39    R1 R1
-   40   C40    R1
-   41   H41    R1
-   42   H42    R1
-   43   H43    R1
-   44   C44    R1
-   45   H45    R1
-   46   H46    R1
-   47   C47   ROH
-   48   H48   ROH
-   49   H49   ROH
-   50   C50    C1 C1 C1 R4
-   51   H51    C1
-   52   C52    C1
-   53   H53    C1
-   54   H54    C1
-   55   H55    C1
-   56   C56    C1
-   57   H57    C1
-   58   H58    C1
-   59   C59    C1 C1 C1 C2
-   60   H60    C1 C1 C1 C2
-   61   H61    C1 C1 C1 C2
-   62   C62    C2 C1
-   63   H63    C2 C1
-   64   H64    C2 C1
-   65   C65    C2 C2 C2 C1
-   66   H66    C2 C2 C2 C1
-   67   C67    C2
-   68   H68    C2
-   69   H69    C2
-   70   H70    C2
-   71   C71    C2
-   72   H72    C2
-   73   H73    C2
-   74   H74    C2
-
-[chiral]
-H4 C1 C5 O2 C47
-H15 C14 C11 C16 C37
-H17 C16 C18 C14 C26
-H38 C37 C39 C34 C14
-H25 C24 C21 C26 C50
-[out]
-C52 C50 C56 C24
-H53 C50 C56 C24
-H54 C50 C56 C24
-H44 C50 C56 C24
-[chiral]
-H51 C50 C24 C52 C56
-
-[chiral]
-C27 C26 C31 C16 C24
-H28 C26 C31 C16 C24
-H29 C26 C31 C16 C24
-H30 C26 C31 C16 C24
-
-[out]
-C47 C1 O2 C5
-H48 C1 O2 C5
-H49 C1 O2 C5
-[trans]
-C44 C47 C1 O2
-H45 C47 C1 O2
-H46 C47 C1 O2
-
-[chiral]
-C40 C39 C44 C8 C37
-H41 C39 C44 C8 C37
-H42 C39 C44 C8 C37
-H43 C39 C44 C8 C37
diff --git a/vermouth/data/mappings/elnedyn/cys.charmm36.map b/vermouth/data/mappings/elnedyn/cys.charmm36.map
old mode 100755
new mode 100644
index 34fd24620..3904d4525
--- a/vermouth/data/mappings/elnedyn/cys.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/cys.charmm36.map
@@ -19,7 +19,7 @@ CYS
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 elnedyn22p
 
diff --git a/vermouth/data/mappings/elnedyn/dmpc.charmm36.map b/vermouth/data/mappings/elnedyn/dmpc.charmm36.map
deleted file mode 100644
index 31992bbb8..000000000
--- a/vermouth/data/mappings/elnedyn/dmpc.charmm36.map
+++ /dev/null
@@ -1,197 +0,0 @@
-; Copyright 2018 University of Groningen
-;
-; Licensed under the Apache License, Version 2.0 (the "License");
-; you may not use this file except in compliance with the License.
-; You may obtain a copy of the License at
-;
-;    http://www.apache.org/licenses/LICENSE-2.0
-;
-; Unless required by applicable law or agreed to in writing, software
-; distributed under the License is distributed on an "AS IS" BASIS,
-; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-; See the License for the specific language governing permissions and
-; limitations under the License.
-
-[ molecule ]
-DMPC
-
-[from]
-universal
-
-[to]
-elnedyn
-elnedyn22
-elnedyn22p
-
-; Mapping file created 24/11/2015 by Kri
-
-[ martini ]
-NC3 PO4 GL1 GL2 C1A C2A C3A C1B C2B C3B
-;
-; NC3-PO4-GL1-C1A-C2A-C3A
-;         |
-;         GL2-C1B-C2B-C3B
-
-[ mapping ]
-charmm charmm27 charmm36
-
-[ atoms ]
-; Terminal head group (choline)
-    1     N   NC3 
-    2   C13   NC3 
-    3  H13A   NC3 
-    4  H13B   NC3 
-    5  H13C   NC3 
-    6   C14   NC3 
-    7  H14A   NC3 
-    8  H14B   NC3 
-    9  H14C   NC3 
-   10   C15   NC3
-   11  H15A   NC3
-   12  H15B   NC3
-   13  H15C   NC3
-   14   C12   NC3 NC3 NC3 PO4 
-   15  H12A   NC3 NC3 NC3 PO4
-   16  H12B   NC3 NC3 NC3 PO4
-   17   C11   NC3 PO4 
-   18  H11A   NC3 PO4 
-   19  H11B   NC3 PO4 
-; Phosphate group 
-   20     P   PO4
-   21   O13   PO4 
-   22   O14   PO4
-   23   O11   PO4 PO4 GL1
-   24   O12   PO4 PO4 PO4 NC3
-; Diacylglycerol
-   25    C1   GL1 GL1 PO4
-   26    HA   GL1 GL1 PO4
-   27    HB   GL1 GL1 PO4
-   28    C2   GL1 GL1 GL2 
-   29    HS   GL1 GL1 GL2
-   30   O21   GL1 GL1 GL2 C1A
-   31   C21   GL1 C1A
-   32   O22   GL1
-   33   C22   C1A C1A GL1
-   34   H2R   C1A C1A GL1
-   35   H2S   C1A C1A GL1
-   36    C3   GL2 GL2 GL2 PO4
-   37    HX   GL2 GL2 GL2 PO4
-   38    HY   GL2 GL2 GL2 PO4
-   39   O31   GL2
-   40   C31   GL2 GL2 C1B
-   41   O32   GL2
-   42   C32   C1B C1B GL2
-   43   H2X   C1B C1B GL2
-   44   H2Y   C1B C1B GL2
-   45   C23   C1A
-   46   H3R   
-   47   H3S   
-   48   C24   C1A C1A C1A C1A C2A
-   49   H4R   
-   50   H4S   
-   51   C25   C1A C1A C1A C2A C2A
-   52   H5R   
-   53   H5S   
-   54   C26   C1A C1A C2A C2A C2A
-   55   H6R   
-   56   H6S   
-   57   C27   C1A C2A C2A C2A C2A
-   58   H7R   
-   59   H7S   
-   60   C28   C2A
-   61   H8R   
-   62   H8S   
-   63   C29   C2A C2A C2A C2A C3A
-   64   H9R   
-   65   H9S   
-   66  C210   C2A C2A C2A C3A C3A
-   67  H10R   
-   68  H10S   
-   69  C211   C2A C2A C3A C3A C3A
-   70  H11R   
-   71  H11S   
-   72  C212   C2A C3A C3A C3A C3A
-   73  H12R   
-   74  H12S   
-   75  C213   C3A
-   76  H13R   
-   77  H13S   
-   78  C214   
-   79  H14R   
-   80  H14S   
-   87  H14T   
-   88   C33   C1B
-   89   H3X   
-   90   H3Y   
-   91   C34   C1B C1B C1B C1B C2B
-   92   H4X   
-   93   H4Y   
-   94   C35   C1B C1B C1B C2B C2B 
-   95   H5X   
-   96   H5Y   
-   97   C36   C1B C1B C2B C2B C2B 
-   98   H6X   
-   99   H6Y   
-  100   C37   C1B C2B C2B C2B C2B 
-  101   H7X   
-  102   H7Y   
-  103   C38   C2B
-  104   H8X   
-  105   H8Y   
-  106   C39   C2B C2B C2B C2B C3B 
-  107   H9X   
-  108   H9Y   
-  109  C310   C2B C2B C2B C3B C3B 
-  110  H10X   
-  111  H10Y   
-  112  C311   C2B C2B C3B C3B C3B 
-  113  H11X   
-  114  H11Y   
-  115  C312   C2B C3B C3B C3B C3B 
-  116  H12X   
-  117  H12Y   
-  118  C313   C3B
-  119  H13X   
-  120  H13Y   
-  121  C314   
-  122  H14X   
-  123  H14Y   
-  130  H14Z   
-
-;;;making a choline group
-[out]
-C14 N C13 C12
-H14A N C13 C12
-H14B N C13 C12
-H14C N C13 C12
-
-[ chiral ]
-C15 N C12 C13 C14
-H15A N C12 C13 C14
-H15B N C12 C13 C14
-H15C N C12 C13 C14
-
-;making R stereoisomer- placing HS
-[chiral]
-HS C2 O21 C1 C3
-
-; acyl esters
-[trans]
-C22 C21 O21 C2
-[ out ]
-O22 C21 O21 C22
-[trans]
-C32 C31 O31 C3
-[out]
-O32 C31 O31 C32
-
-; extend chains by one
-[ trans ]
-C214 C213 C212 C211
-H14R C213 C212 C211
-H14S C213 C212 C211
-H14T C213 C212 C211
-C314 C313 C312 C212
-H14X C313 C312 C311
-H14Y C313 C312 C311
-H14Z C313 C312 C311
diff --git a/vermouth/data/mappings/elnedyn/dopc.charmm36.map b/vermouth/data/mappings/elnedyn/dopc.charmm36.map
deleted file mode 100644
index 1f97a3544..000000000
--- a/vermouth/data/mappings/elnedyn/dopc.charmm36.map
+++ /dev/null
@@ -1,222 +0,0 @@
-; Copyright 2018 University of Groningen
-;
-; Licensed under the Apache License, Version 2.0 (the "License");
-; you may not use this file except in compliance with the License.
-; You may obtain a copy of the License at
-;
-;    http://www.apache.org/licenses/LICENSE-2.0
-;
-; Unless required by applicable law or agreed to in writing, software
-; distributed under the License is distributed on an "AS IS" BASIS,
-; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-; See the License for the specific language governing permissions and
-; limitations under the License.
-
-[ molecule ]
-DOPC
-
-[from]
-universal
-
-[to]
-elnedyn
-elnedyn22
-elnedyn22p
-
-; Mapping file created 15/03/2013 by Kri
-
-;
-; NC3-PO4-GL1-C1A-C2A-D3A-C4A-C5A
-;         |
-;         GL2-C1B-C2B-D3B-C4B-C5B
-
-[ martini ]
-NC3 PO4 GL1 GL2 C1A C2A D3A C4A C5A C1B C2B D3B C4B C5B
-
-[ mapping ]
-charmm27 charmm36
-
-[ atoms ]
-; Terminal head group (choline)
-    1     N   NC3 
-    2   C12   NC3 NC3 NC3 PO4 
-    3   C13   NC3 
-    4   C14   NC3 
-    5   C15   NC3
-    6  H12A   NC3 NC3 NC3 PO4
-    7  H12B   NC3 NC3 NC3 PO4
-    8  H13A   NC3 
-    9  H13B   NC3 
-   10  H13C   NC3 
-   11  H14A   NC3 
-   12  H14B   NC3 
-   13  H14C   NC3 
-   14  H15A   NC3
-   15  H15B   NC3
-   16  H15C   NC3
-   17   C11   NC3 PO4  
-   18  H11A   NC3 PO4
-   19  H11B   NC3 PO4
-; Phosphate group 
-   20     P   PO4
-   21   O13   PO4 
-   22   O14   PO4
-   23   O12   PO4 PO4 PO4 NC3
-   24   O11   PO4 PO4 GL1
-; Diacylglycerol
-   25    C1   GL1 GL1 PO4
-   26    HA   GL1 GL1 PO4
-   27    HB   GL1 GL1 PO4
-   28    C2   GL1 GL1 GL2
-   29    HS   GL1 GL1 GL2
-   30   O21   GL1 GL1 GL2 C1A
-   31   C21   GL1 C1A
-   32   O22   GL1
-   33   C22   C1A C1A GL1
-   34   H2R   C1A C1A GL1
-   35   H2S   C1A C1A GL1
-   36    C3   GL2 GL2 GL2 PO4
-   37    HX   GL2 GL2 GL2 PO4
-   38    HY   GL2 GL2 GL2 PO4
-   39   O31   GL2
-   40   C31   GL2 GL2 C1B
-   41   O32   GL2
-   42   C32   C1B C1B GL2
-   43   H2X   C1B C1B GL2
-   44   H2Y   C1B C1B GL2
-   45   C23   C1A
-   46   H3R   C1A
-   47   H3S   C1A
-   48   C24   C1A C1A C2A
-   49   H4R   C1A C1A C2A
-   50   H4S   C1A C1A C2A
-   51   C25   C1A C2A
-   52   H5R   C1A C2A
-   53   H5S   C1A C2A
-   54   C26   C2A C2A C1A
-   55   H6R   C2A C2A C1A
-   56   H6S   C2A C2A C1A
-   57   C27   C2A
-   58   H7R   C2A
-   59   H7S   C2A
-   60   C28   C2A D3A
-   61   H8R   C2A D3A
-   62   H8S   C2A D3A
-   63   C29   D3A D3A C2A
-   64   H9R   D3A
-   65  C210   D3A D3A C4A
-   66  H10R   D3A
-   67  C211   D3A
-   68  H11R   D3A C4A
-   69  H11S   D3A C4A
-   70  C212   C4A
-   71  H12R   C4A
-   72  H12S   C4A
-   73  C213   C4A C4A C4A C5A
-   74  H13R   C4A C4A C4A C5A
-   75  H13S   C4A C4A C4A C5A
-   76  C214   C4A C4A C5A
-   77  H14R   C4A C4A C5A
-   78  H14S   C4A C4A C5A
-   79  C215   C5A C4A
-   80  H15R   C5A C4A
-   81  H15S   C5A C4A
-   82  C216   C5A C5A C4A
-   83  H16R   C5A C5A C4A
-   84  H16S   C5A C5A C4A
-   85  C217   C5A C5A C5A C4A
-   86  H17R   C5A C5A C5A C4A
-   87  H17S   C5A C5A C5A C4A
-   88  C218   C5A
-   89  H18R   C5A
-   90  H18S   C5A
-   91  H18T   C5A
-   92   C33   C1B
-   93   H3X   C1B
-   94   H3Y   C1B
-   95   C34   C1B C1B C2B
-   96   H4X   C1B C1B C2B
-   97   H4Y   C1B C1B C2B
-   98   C35   C1B C2B
-   99   H5X   C1B C2B
-  100   H5Y   C1B C2B
-  101   C36   C2B C2B C1B
-  102   H6X   C2B C2B C1B
-  103   H6Y   C2B C2B C1B
-  104   C37   C2B
-  105   H7X   C2B
-  106   H7Y   C2B
-  107   C38   C2B D3B
-  108   H8X   C2B D3B
-  109   H8Y   C2B D3B
-  110   C39   D3B D3B C2B
-  111   H9X   D3B D3B C2B
-  112  C310   D3B D3B C4B
-  113  H10X   D3B D3B C4B
-  114  C311   D3B C4B
-  115  H11X   D3B C4B
-  116  H11Y   D3B C4B
-  117  C312   C4B
-  118  H12X   C4B
-  119  H12Y   C4B
-  120  C313   C4B C4B C4B C5B
-  121  H13X   C4B C4B C4B C5B
-  122  H13Y   C4B C4B C4B C5B
-  123  C314   C4B C4B C5B
-  124  H14X   C4B C4B C5B
-  125  H14Y   C4B C4B C5B
-  126  C315   C5B C4B
-  127  H15X   C5B C4B
-  128  H15Y   C5B C4B
-  129  C316   C5B C5B C4B
-  130  H16X   C5B C5B C4B
-  131  H16Y   C5B C5B C4B
-  132  C317   C5B C5B C5B C4B
-  133  H17X   C5B C5B C5B C4B
-  134  H17Y   C5B C5B C5B C4B
-  135  C318   C5B
-  136  H18X   C5B
-  137  H18Y   C5B
-  138  H18Z   C5B
-
-;making R stereoisomer- placing HS
-[chiral]
-HS C2 O21 C1 C3
-
-; acyl esters
-[trans]
-C22 C21 O21 C2
-[ out ]
-O22 C21 O21 C22
-[trans]
-C32 C31 O31 C3
-[out] 
-O32 C31 O31 C32
-
-;cis bonds in lipind chains
-[ out ]
-H9R C29 C28 C210
-[ trans ] 
-H10R C210 C29 C28
-[ out ]
-C211 C210 C29 H10R
-
-[ out ]
-H9X C39 C38 C310
-[ trans ]
-H10X C310 C39 C38
-[ out ]
-C311 C310 C39 H10X
-
-;;;making a choline group
-[out]
-C14 N C13 C12
-H14A N C13 C12
-H14B N C13 C12
-H14C N C13 C12
-
-[ chiral ]
-C15 N C12 C13 C14
-H15A N C12 C13 C14
-H15B N C12 C13 C14
-H15C N C12 C13 C14
diff --git a/vermouth/data/mappings/elnedyn/dppc.charmm36.map b/vermouth/data/mappings/elnedyn/dppc.charmm36.map
deleted file mode 100644
index 1b6dfeef9..000000000
--- a/vermouth/data/mappings/elnedyn/dppc.charmm36.map
+++ /dev/null
@@ -1,198 +0,0 @@
-; Copyright 2018 University of Groningen
-;
-; Licensed under the Apache License, Version 2.0 (the "License");
-; you may not use this file except in compliance with the License.
-; You may obtain a copy of the License at
-;
-;    http://www.apache.org/licenses/LICENSE-2.0
-;
-; Unless required by applicable law or agreed to in writing, software
-; distributed under the License is distributed on an "AS IS" BASIS,
-; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-; See the License for the specific language governing permissions and
-; limitations under the License.
-
-[ molecule ]
-DPPC
-
-[from]
-universal
-
-[to]
-elnedyn
-elnedyn22
-elnedyn22p
-
-; Mapping file created 28/02/2013 by Kri
-
-[ martini ]
-NC3 PO4 GL1 GL2 C1A C2A C3A C4A C1B C2B C3B C4B 
-;
-; NC3-PO4-GL1-C1A-C2A-C3A-C4A
-;         |
-;         GL2-C1B-C2B-C3B-C4B
-
-[ mapping ]
-charmm27 charmm36
-
-[ atoms ]
-; Terminal head group (choline)
-    1     N   NC3 
-    2   C13   NC3 
-    3  H13A   NC3 
-    4  H13B   NC3 
-    5  H13C   NC3 
-    6   C14   NC3 
-    7  H14A   NC3 
-    8  H14B   NC3 
-    9  H14C   NC3 
-   10   C15   NC3
-   11  H15A   NC3
-   12  H15B   NC3
-   13  H15C   NC3
-   14   C12   NC3 NC3 NC3 PO4 
-   15  H12A   NC3 NC3 NC3 PO4
-   16  H12B   NC3 NC3 NC3 PO4
-   17   C11   NC3 PO4 
-   18  H11A   NC3 PO4 
-   19  H11B   NC3 PO4 
-; Phosphate group 
-   20     P   PO4
-   21   O13   PO4 
-   22   O14   PO4
-   23   O11   PO4 PO4 GL1
-   24   O12   PO4 PO4 PO4 NC3
-; Diacylglycerol
-   25    C1   GL1 GL1 PO4
-   26    HA   GL1 GL1 PO4
-   27    HB   GL1 GL1 PO4
-   28    C2   GL1 GL1 GL2 
-   29    HS   GL1 GL1 GL2
-   30   O21   GL1 GL1 GL2 C1A
-   31   C21   GL1 C1A
-   32   O22   GL1
-   33   C22   C1A C1A GL1
-   34   H2R   C1A C1A GL1
-   35   H2S   C1A C1A GL1
-   36    C3   GL2 GL2 GL2 PO4
-   37    HX   GL2 GL2 GL2 PO4
-   38    HY   GL2 GL2 GL2 PO4
-   39   O31   GL2
-   40   C31   GL2 GL2 C1B
-   41   O32   GL2
-   42   C32   C1B C1B GL2
-   43   H2X   C1B C1B GL2
-   44   H2Y   C1B C1B GL2
-   45   C23   C1A
-   46   H3R   C1A
-   47   H3S   C1A
-   48   C24   C1A C1A C2A
-   49   H4R   C1A C1A C2A
-   50   H4S   C1A C1A C2A
-   51   C25   C1A C2A
-   52   H5R   C1A C2A
-   53   H5S   C1A C2A
-   54   C26   C2A C2A C1A
-   55   H6R   C2A C2A C1A
-   56   H6S   C2A C2A C1A
-   57   C27   C2A
-   58   H7R   C2A
-   59   H7S   C2A
-   60   C28   C2A C2A C2A C3A
-   61   H8R   C2A C2A C2A C3A
-   62   H8S   C2A C2A C2A C3A
-   63   C29   C2A C2A C3A
-   64   H9R   C2A C2A C3A
-   65   H9S   C2A C2A C3A
-   66  C210   C3A C2A
-   67  H10R   C3A C2A
-   68  H10S   C3A C2A
-   69  C211   C3A C3A C2A
-   70  H11R   C3A C3A C2A
-   71  H11S   C3A C3A C2A
-   72  C212   C3A
-   73  H12R   C3A
-   74  H12S   C3A
-   75  C213   C3A C3A C4A
-   76  H13R   C3A C3A C4A
-   77  H13S   C3A C3A C4A
-   78  C214   C4A C3A
-   79  H14R   C4A C3A
-   80  H14S   C4A C3A
-   81  C215   C4A C4A C3A
-   82  H15R   C4A C4A C3A
-   83  H15S   C4A C4A C3A
-   84  C216   C4A
-   85  H16R   C4A
-   86  H16S   C4A
-   87  H16T   C4A
-   88   C33   C1B
-   89   H3X   C1B
-   90   H3Y   C1B
-   91   C34   C1B C1B C2B
-   92   H4X   C1B C1B C2B
-   93   H4Y   C1B C1B C2B
-   94   C35   C1B C2B
-   95   H5X   C1B C2B
-   96   H5Y   C1B C2B
-   97   C36   C2B C2B C1B
-   98   H6X   C2B C2B C1B
-   99   H6Y   C2B C2B C1B
-  100   C37   C2B
-  101   H7X   C2B
-  102   H7Y   C2B
-  103   C38   C2B C2B C2B C3B
-  104   H8X   C2B C2B C2B C3B
-  105   H8Y   C2B C2B C2B C3B
-  106   C39   C2B C2B C3B
-  107   H9X   C2B C2B C3B
-  108   H9Y   C2B C2B C3B
-  109  C310   C3B C2B
-  110  H10X   C3B C2B
-  111  H10Y   C3B C2B
-  112  C311   C3B C3B C2B
-  113  H11X   C3B C3B C2B
-  114  H11Y   C3B C3B C2B
-  115  C312   C3B
-  116  H12X   C3B
-  117  H12Y   C3B
-  118  C313   C3B C3B C4B
-  119  H13X   C3B C3B C4B
-  120  H13Y   C3B C3B C4B
-  121  C314   C4B C3B
-  122  H14X   C4B C3B
-  123  H14Y   C4B C3B
-  124  C315   C4B C4B C3B
-  125  H15X   C4B C4B C3B
-  126  H15Y   C4B C4B C3B
-  127  C316   C4B
-  128  H16X   C4B
-  129  H16Y   C4B
-  130  H16Z   C4B
-
-;;;making a choline group
-[out]
-C14 N C13 C12
-H14A N C13 C12
-H14B N C13 C12
-H14C N C13 C12
-
-[ chiral ]
-C15 N C12 C13 C14
-H15A N C12 C13 C14
-H15B N C12 C13 C14
-H15C N C12 C13 C14
-
-;making R stereoisomer- placing HS
-[chiral]
-HS C2 O21 C1 C3
-
-; acyl esters
-[trans]
-C22 C21 O21 C2
-[ out ]
-O22 C21 O21 C22
-[trans]
-C32 C31 O31 C3
-[out]
-O32 C31 O31 C32
diff --git a/vermouth/data/mappings/elnedyn/dppg.charmm36.map b/vermouth/data/mappings/elnedyn/dppg.charmm36.map
deleted file mode 100644
index 9cd25ac46..000000000
--- a/vermouth/data/mappings/elnedyn/dppg.charmm36.map
+++ /dev/null
@@ -1,181 +0,0 @@
-; Copyright 2018 University of Groningen
-;
-; Licensed under the Apache License, Version 2.0 (the "License");
-; you may not use this file except in compliance with the License.
-; You may obtain a copy of the License at
-;
-;    http://www.apache.org/licenses/LICENSE-2.0
-;
-; Unless required by applicable law or agreed to in writing, software
-; distributed under the License is distributed on an "AS IS" BASIS,
-; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-; See the License for the specific language governing permissions and
-; limitations under the License.
-
-[ molecule ]
-DPPG
-
-[from]
-universal
-
-[to]
-elnedyn
-elnedyn22
-elnedyn22p
-
-; Created by Jagannath Mondal
-
-[ martini ]
-GL0 PO4 GL1 GL2 C1A C2A C3A C4A C1B C2B C3B C4B 
-
-[ mapping ]
-charmm36
-
-[ atoms ]
-1	C13	GL0			
-2	H13A	GL0			
-3	H13B	GL0			
-4	OC3	GL0			
-5	HO3	GL0			
-6	C12	GL0	GL0	GL0	PO4
-7	H12A	GL0			
-8	OC2	GL0			
-9	HO2	GL0			
-10	C11	GL0	PO4		
-11	H11A	GL0	PO4		
-12	H11B	GL0	PO4		
-13	P	PO4			
-14	O13	PO4			
-15	O14	PO4			
-16	O12	PO4	PO4	PO4	GL0
-17	O11	PO4	PO4	GL1	
-18	C1	GL1	GL1	PO4	
-19	HA	GL1	GL1	PO4	
-20	HB	GL1	GL1	PO4	
-21	C2	GL1	GL1	GL2	
-22	HS	GL1	GL1	GL2	
-23	O21	GL1	GL1	GL2	C1B
-24	C21	GL1	C1B		
-25	O22	GL1			
-26	C22	C1B	C1B	GL1	
-27	H2R	C1B	C1B	GL1	
-28	H2S	C1B	C1B	GL1	
-29	C3	GL2	GL2	GL2	PO4
-30	HX	GL2	GL2	GL2	PO4
-31	HY	GL2	GL2	GL2	PO4
-32	O31	GL2			
-33	C31	GL2	GL1	C1A	
-34	O32	GL2			
-35	C32	C1A	C1A	GL2	
-36	H2X	C1A	C1A	GL2	
-37	H2Y	C1A	C1A	GL2	
-38	C23	C1A			
-39	H3R	C1A			
-40	H3S	C1A			
-41	C24	C1A	C1A	C2A	
-42	H4R	C1A	C1A	C2A	
-43	H4S	C1A	C1A	C2A	
-44	C25	C1A	C2A		
-45	H5R	C1A	C2A		
-46	H5S	C1A	C2A		
-47	C26	C2A	C2A	C1A	
-48	H6R	C2A	C2A	C1A	
-49	H6S	C2A	C2A	C1A	
-50	C27	C2A			
-51	H7R	C2A			
-52	H7S	C2A			
-53	C28	C2A	C3A		
-54	H8R	C2A	C3A		
-55	H8S	C2A	C3A		
-56	C29	C2A	C2A	C3A	
-57	H9R	C2A	C2A	C3A	
-58	H9S	C2A	C2A	C3A	
-59	C210	C3A	C2A		
-60	H10R	C3A	C2A		
-61	H10S	C3A	C2A		
-62	C211	C3A	C3A	C2A	
-63	H11R	C3A	C3A	C2A	
-64	H11S	C3A	C3A	C2A	
-65	C212	C3A			
-66	H12R	C3A			
-67	H12S	C3A			
-68	C213	C3A	C3A	C4A	
-69	H13R	C3A	C3A	C4A	
-70	H13S	C3A	C3A	C4A	
-71	C214	C4A	C3A		
-72	H14R	C4A	C3A		
-73	H14S	C4A	C3A		
-74	C215	C4A	C4A	C3A	
-75	H15R	C4A	C4A	C3A	
-76	H15S	C4A	C4A	C3A	
-77	C216	C4A			
-78	H16R	C4A			
-79	H16S	C4A			
-80	H16T	C4A			
-81	C33	C1B			
-82	H3X	C1B			
-83	H3Y	C1B			
-84	C34	C1B	C1B	C2B	
-85	H4X	C1B	C1B	C2B	
-86	H4Y	C1B	C1B	C2B	
-87	C35	C1B	C2B		
-88	H5X	C1B	C2B		
-89	H5Y	C1B	C2B		
-90	C36	C2B	C2B	C1B	
-91	H6X	C2B	C2B	C1B	
-92	H6Y	C2B	C2B	C1B	
-93	C37	C2B			
-94	H7X	C2B			
-95	H7Y	C2B			
-96	C38	C2B	C2B	C2B	C3B
-97	H8X	C2B	C2B	C2B	C3B
-98	H8Y	C2B	C2B	C2B	C3B
-99	C39	C2B	C2B	C3B	
-100	H9X	C2B	C2B	C3B	
-101	H9Y	C2B	C2B	C3B	
-102	C310	C3B	C2B		
-103	H10X	C3B	C2B		
-104	H10Y	C3B	C2B		
-105	C311	C3B	C3B	C2B	
-106	H11X	C3B	C3B	C2B	
-107	H11Y	C3B	C3B	C2B	
-108	C312	C3B			
-109	H12X	C3B			
-110	H12Y	C3B			
-111	C313	C3B	C3B	C4B	
-112	H13X	C3B	C3B	C4B	
-113	H13Y	C3B	C3B	C4B	
-114	C314	C4B	C3B		
-115	H14X	C4B	C3B		
-116	H14Y	C4B	C3B		
-117	C315	C4B	C4B	C3B	
-118	H15X	C4B	C4B	C3B	
-119	H15Y	C4B	C4B	C3B	
-120	C316	C4B			
-121	H16X	C4B			
-122	H16Y	C4B			
-123	H16Z	C4B			
-
-;making R stereoisomer- placing HS
-[chiral]
-HS C2 O21 C1 C3
-
-; acyl esters
-[trans]
-C22 C21 O21 C2
-[ out ]
-O22 C21 O21 C22
-[trans]
-C32 C31 O31 C3
-[out]
-O32 C31 O31 C32
-
-;;;making a glycerol headgroup
-[trans]
-HO3 OC3 C13 C12
-[out]
-OC2 C12 HO3 C11
-[chiral]
-H12A C12 OC2 C13 C11
-OC2 C12 C11 C13 H12A
-HO2 C12 C11 C13 H12A
diff --git a/vermouth/data/mappings/elnedyn/gln.charmm36.map b/vermouth/data/mappings/elnedyn/gln.charmm36.map
index 0c80c8154..36916484d 100644
--- a/vermouth/data/mappings/elnedyn/gln.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/gln.charmm36.map
@@ -19,7 +19,7 @@ GLN
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 
 [ martini ]
diff --git a/vermouth/data/mappings/elnedyn/glu.charmm36.map b/vermouth/data/mappings/elnedyn/glu.charmm36.map
old mode 100755
new mode 100644
index 49e22593c..f79c56276
--- a/vermouth/data/mappings/elnedyn/glu.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/glu.charmm36.map
@@ -19,7 +19,7 @@ GLU
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 
 [ martini ]
diff --git a/vermouth/data/mappings/elnedyn/gly.charmm36.map b/vermouth/data/mappings/elnedyn/gly.charmm36.map
old mode 100755
new mode 100644
index dd98285da..3ac6ed796
--- a/vermouth/data/mappings/elnedyn/gly.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/gly.charmm36.map
@@ -19,7 +19,7 @@ GLY
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 elnedyn22p
 
diff --git a/vermouth/data/mappings/elnedyn/his.charmm36.map b/vermouth/data/mappings/elnedyn/his.charmm36.map
index 81f13b0dc..5ad2aabff 100644
--- a/vermouth/data/mappings/elnedyn/his.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/his.charmm36.map
@@ -19,7 +19,7 @@ HIS  ;;;; is in fact HSP but if one of hydrogen on a nitrogen is missing in the
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 elnedyn22p
 
diff --git a/vermouth/data/mappings/elnedyn/ile.charmm36.map b/vermouth/data/mappings/elnedyn/ile.charmm36.map
index 7d333ea37..f165065e4 100644
--- a/vermouth/data/mappings/elnedyn/ile.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/ile.charmm36.map
@@ -19,7 +19,7 @@ ILE
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 elnedyn22p
 
diff --git a/vermouth/data/mappings/elnedyn/leu.charmm36.map b/vermouth/data/mappings/elnedyn/leu.charmm36.map
index 56eaffe82..690254085 100644
--- a/vermouth/data/mappings/elnedyn/leu.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/leu.charmm36.map
@@ -19,7 +19,7 @@ LEU
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 elnedyn22p
 
diff --git a/vermouth/data/mappings/elnedyn/lys.charmm36.map b/vermouth/data/mappings/elnedyn/lys.charmm36.map
index e2d06843c..f728eefae 100644
--- a/vermouth/data/mappings/elnedyn/lys.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/lys.charmm36.map
@@ -19,7 +19,7 @@ LYS
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 
 [ martini ]
diff --git a/vermouth/data/mappings/elnedyn/met.charmm36.map b/vermouth/data/mappings/elnedyn/met.charmm36.map
old mode 100755
new mode 100644
index 4b44eb944..f9685a7df
--- a/vermouth/data/mappings/elnedyn/met.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/met.charmm36.map
@@ -19,7 +19,7 @@ MET
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 elnedyn22p
 
diff --git a/vermouth/data/mappings/elnedyn/modifications.elnedyn21.mapping b/vermouth/data/mappings/elnedyn/modifications.elnedyn21.mapping
new file mode 100644
index 000000000..6799b7d87
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn/modifications.elnedyn21.mapping
@@ -0,0 +1,105 @@
+[ modification ]
+[ from ]
+universal
+[ to ]
+elnedyn21
+
+[ from blocks ]
+C-ter
+[ to blocks ]
+C-ter
+
+[ from nodes ]
+N
+HN
+
+[ from edges ]
+HN N
+N CA
+
+[ mapping ]
+CA BB
+C  BB 0
+O  BB 0
+OXT BB 0
+
+
+[modification]
+[ from ]
+universal
+[ to ]
+elnedyn21
+[ from blocks ]
+N-ter
+[ to blocks ]
+N-ter
+
+[ from nodes ]
+C
+O
+
+[ from edges ]
+C O
+CA C
+
+[ mapping ]
+HN2 BB 0
+HN3 BB 0
+N   BB 0
+CA  BB
+C   BB 0
+O   BB 0
+
+[ modification ]
+[ from ]
+universal
+[ to ]
+elnedyn21
+
+[ from blocks ]
+COOH-ter
+[ to blocks ]
+COOH-ter
+
+[ from nodes ]
+N
+HN
+
+[ from edges ]
+HN N
+N CA
+
+[ mapping ]
+HN BB 0
+N BB 0
+CA BB
+C  BB 0
+O  BB 0
+HO BB 0
+OXT BB 0
+
+
+[modification]
+[ from ]
+universal
+[ to ]
+elnedyn21
+[ from blocks ]
+NH2-ter
+[ to blocks ]
+NH2-ter
+
+[ from nodes ]
+C
+O
+
+[ from edges ]
+C O
+CA C
+
+[ mapping ]
+HN2 BB 0
+N   BB 0
+CA  BB
+C   BB 0
+O   BB 0
diff --git a/vermouth/data/mappings/elnedyn/elnedyn22/modifications.mapping b/vermouth/data/mappings/elnedyn/modifications.elnedyn22.mapping
similarity index 99%
rename from vermouth/data/mappings/elnedyn/elnedyn22/modifications.mapping
rename to vermouth/data/mappings/elnedyn/modifications.elnedyn22.mapping
index f2fa69e70..06bda49e8 100644
--- a/vermouth/data/mappings/elnedyn/elnedyn22/modifications.mapping
+++ b/vermouth/data/mappings/elnedyn/modifications.elnedyn22.mapping
@@ -104,7 +104,6 @@ CA  BB
 C   BB 0
 O   BB 0
 
-
 [modification]
 [ from ]
 universal
diff --git a/vermouth/data/mappings/elnedyn/elnedyn22p/modifications.mapping b/vermouth/data/mappings/elnedyn/modifications.elnedyn22p.mapping
similarity index 100%
rename from vermouth/data/mappings/elnedyn/elnedyn22p/modifications.mapping
rename to vermouth/data/mappings/elnedyn/modifications.elnedyn22p.mapping
diff --git a/vermouth/data/mappings/elnedyn/phe.charmm36.map b/vermouth/data/mappings/elnedyn/phe.charmm36.map
index 2b166f336..8ffd2a4f1 100644
--- a/vermouth/data/mappings/elnedyn/phe.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/phe.charmm36.map
@@ -19,7 +19,7 @@ PHE
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 elnedyn22p
 
diff --git a/vermouth/data/mappings/elnedyn/popc.charmm36.map b/vermouth/data/mappings/elnedyn/popc.charmm36.map
deleted file mode 100644
index 291e4b736..000000000
--- a/vermouth/data/mappings/elnedyn/popc.charmm36.map
+++ /dev/null
@@ -1,229 +0,0 @@
-; Copyright 2018 University of Groningen
-;
-; Licensed under the Apache License, Version 2.0 (the "License");
-; you may not use this file except in compliance with the License.
-; You may obtain a copy of the License at
-;
-;    http://www.apache.org/licenses/LICENSE-2.0
-;
-; Unless required by applicable law or agreed to in writing, software
-; distributed under the License is distributed on an "AS IS" BASIS,
-; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-; See the License for the specific language governing permissions and
-; limitations under the License.
-
-; latest revision TAW 20160213
-[ molecule ]
-POPC
-
-[from]
-universal
-
-[to]
-elnedyn
-elnedyn22
-elnedyn22p
-
-[ martini ]
-NC3 PO4 GL1 GL2 C1A D2A C3A C4A C1B C2B C3B C4B 
-
-[ mapping ]
-charmm27 charmm36 slipids amber
-
-[ atoms ]
-    1     N   NC3
-    2   C12   NC3 NC3 NC3 PO4
-    3   C13   NC3
-    4   C14   NC3
-    5   C15   NC3
-    6  H12A   NC3 NC3 NC3 PO4
-    7  H12B   NC3 NC3 NC3 PO4
-    8  H13A   NC3
-    9  H13B   NC3
-   10  H13C   NC3
-   11  H14A   NC3
-   12  H14B   NC3
-   13  H14C   NC3
-   14  H15A   NC3
-   15  H15B   NC3
-   16  H15C   NC3
-   17   C11   NC3 PO4
-   18  H11A   NC3 PO4
-   19  H11B   NC3 PO4
-   20     P   PO4
-   21   O13   PO4
-   22   O14   PO4
-   23   O12   PO4 PO4 PO4 NC3
-   24   O11   PO4 PO4 GL1
-   25    C1   GL1 GL1 PO4
-   26    HA   GL1 GL1 PO4
-   27    HB   GL1 GL1 PO4
-   28    C2   GL1 GL1 GL2
-   29    HS   GL1 GL1 GL2
-   30   O21   GL1 GL1 GL2 C1A
-   31   C21   GL1 C1A
-   32   O22   GL1
-   33   C22   C1A C1A GL1 
-   34   H2R   C1A C1A GL1
-   35   H2S   C1A C1A GL1
-   36    C3   GL2 GL2 GL2 PO4
-   37    HX   GL2 GL2 GL2 PO4
-   38    HY   GL2 GL2 GL2 PO4
-   39   O31   GL2
-   40   C31   GL2 GL1 C1B
-   41   O32   GL2
-   42   C32   C1B C1B GL2
-   43   H2X   C1B C1B GL2
-   44   H2Y   C1B C1B GL2
-; First tail
-   45   C23   C1A
-   46   H3R   
-   47   H3S   
-   48   C24   C1A C1A C1A D2A
-   49   H4R   
-   50   H4S   
-   51   C25   C1A D2A
-   52   H5R   
-   53   H5S   
-   54   C26   D2A D2A D2A C1A
-   55   H6R   
-   56   H6S   
-   57   C27   D2A
-   58   H7R   
-   59   H7S   
-   60   C28   D2A D2A D2A C3A
-   61   H8R   
-   62   H8S   
-   63   C29   D2A D2A C3A
-   64   H91   D2A C3A
-   65  C210   C3A C3A D2A
-   66  H101   D2A C3A
-   67  C211   C3A C3A C3A D2A
-   68  H11R   
-   69  H11S   
-   70  C212   C3A
-   71  H12R   
-   72  H12S   
-   73  C213   C3A C3A C3A C4A
-   74  H13R   
-   75  H13S   
-   76  C214   C3A C4A
-   77  H14R   
-   78  H14S   
-   79  C215   C4A C4A C4A C3A
-   80  H15R   
-   81  H15S   
-   82  C216   C4A
-   83  H16R   
-   84  H16S   
-   85  C217   C4A
-   86  H17R   
-   87  H17S   
-   88  C218   C4A
-   89  H18R   
-   90  H18S   
-   91  H18T   
-; Other tail
-   92   C33   C1B
-   93   H3X   C1B
-   94   H3Y   C1B
-   95   C34   C1B C1B C2B
-   96   H4X   C1B C1B C2B
-   97   H4Y   C1B C1B C2B
-   98   C35   C1B C2B
-   99   H5X   C1B C2B
-  100   H5Y   C1B C2B
-  101   C36   C2B C2B C1B
-  102   H6X   C2B C2B C1B
-  103   H6Y   C2B C2B C1B
-  104   C37   C2B 
-  105   H7X   C2B
-  106   H7Y   C2B
-  107   C38   C2B C2B C2B C3B
-  108   H8X   C2B C2B C2B C3B
-  109   H8Y   C2B C2B C2B C3B
-  110   C39   C2B C2B C3B
-  111   H9X   C2B C2B C3B
-  112   H9Y   C2B C2B C3B
-  113  C310   C3B C2B 
-  114  H10X   C3B C2B
-  115  H10Y   C3B C2B
-  116  C311   C3B C3B C2B
-  117  H11X   C3B C3B C2B
-  118  H11Y   C3B C3B C2B
-  119  C312   C3B
-  120  H12X   C3B
-  121  H12Y   C3B
-  122  C313   C3B C3B C4B
-  123  H13X   C3B C3B C4B
-  124  H13Y   C3B C3B C4B
-  125  C314   C4B C3B
-  126  H14X   C4B C3B
-  127  H14Y   C4B C3B
-  128  C315   C4B C4B C3B
-  129  H15X   C4B C4B C3B
-  130  H15Y   C4B C4B C3B
-  131  C316   C4B
-  132  H16X   C4B
-  133  H16Y   C4B
-  134  H16Z   C4B
-
-;making R stereoisomer- placing HS
-[chiral]
-HS C2 O21 C1 C3
-
-; acyl esters
-[trans]
-C22 C21 O21 C2
-[ out ]
-O22 C21 O21 C22
-[trans]
-C32 C31 O31 C3
-[out]
-O32 C31 O31 C32
-
-;cis bonds in lipid chains
-;[ out ]
-;H91 C29 C28 C210
-;C210 C29 H91 C28
-;C28 C29 H91 C210
-;[ trans ]
-;C211 C210 C29 H91
-;H101 C210 C29 C28
-;H91 C29 C210 C211
-;C28 C29 C210 H101
-[ out ]
-H7R C27 C26 C28
-H7S C27 C26 C28
-C28 C27 C26 H7R
-[ trans ]
-C29 C28 C27 C26
-C210 C29 C28 C27
-H101 C210 C29 C28
-[ out ]
-C211 C210 H101 C29
-H91 C29 C210 C28
-
-;;;making a choline group
-[out]
-C14 N C13 C12
-H14A N C13 C12
-H14B N C13 C12
-H14C N C13 C12
-
-[ chiral ]
-C15 N C12 C13 C14
-H15A N C12 C13 C14
-H15B N C12 C13 C14
-H15C N C12 C13 C14
-
-; extend the tails
-[ trans ]
-C217 C216 C215 C214
-C17R C216 C215 C214
-C17S C216 C215 C214
-C218 C217 C216 C215
-C18R C217 C216 C215
-C18S C217 C216 C215
-C18T C217 C216 C215
-
diff --git a/vermouth/data/mappings/elnedyn/pope.charmm36.map b/vermouth/data/mappings/elnedyn/pope.charmm36.map
deleted file mode 100644
index aecc7a275..000000000
--- a/vermouth/data/mappings/elnedyn/pope.charmm36.map
+++ /dev/null
@@ -1,185 +0,0 @@
-; Copyright 2018 University of Groningen
-;
-; Licensed under the Apache License, Version 2.0 (the "License");
-; you may not use this file except in compliance with the License.
-; You may obtain a copy of the License at
-;
-;    http://www.apache.org/licenses/LICENSE-2.0
-;
-; Unless required by applicable law or agreed to in writing, software
-; distributed under the License is distributed on an "AS IS" BASIS,
-; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-; See the License for the specific language governing permissions and
-; limitations under the License.
-
-; latest revision kri 15.3.2013
-[ molecule ]
-POPE
-
-[from]
-universal
-
-[to]
-elnedyn
-elnedyn22
-elnedyn22p
-
-[ martini ]
-NH3 PO4 GL1 GL2 C1A C2A C3A C4A C1B C2B D3B C4B C5B
-;
-; NH3-PO4-GL1-C1B-C2B-D3B-C4B-C5B
-;         |
-;         GL2-C1A-C2A-C3A-C4A
-
-
-[ mapping ]
-charmm27 charmm36
-
-[ atoms ]
-    1     N   NH3
-    2   HN1   NH3 
-    3   HN2   NH3
-    4   HN3   NH3
-    5   C12   NH3 NH3 PO4
-    6  H12A   NH3 NH3 PO4
-    7  H12B   NH3 NH3 PO4
-    8   C11   NH3 PO4 PO4
-    9  H11A   NH3 PO4 PO4
-   10  H11B   NH3 PO4 PO4
-   11     P   PO4
-   12   O13   PO4
-   13   O14   PO4
-   14   O12   PO4 PO4 PO4 NH3
-   15   O11   PO4 PO4 GL1
-   16    C1   GL1 GL1 PO4
-   17    HA   GL1 GL1 PO4
-   18    HB   GL1 GL1 PO4
-   19    C2   GL1 GL1 GL2
-   20    HS   GL1 GL1 GL2
-   21   O21   GL1 GL1 GL2 C1B
-   22   C21   GL1 C1B
-   23   O22   GL1
-   24   C22   C1B C1B GL1 
-   25   H2R   C1B C1B GL1
-   26   H2S   C1B C1B GL1
-   27    C3   GL2 GL2 GL2 PO4
-   28    HX   GL2 GL2 GL2 PO4
-   29    HY   GL2 GL2 GL2 PO4
-   30   O31   GL2
-   31   C31   GL2 GL1 C1A
-   32   O32   GL2
-   33   C32   C1A C1A GL2
-   34   H2X   C1A C1A GL2
-   35   H2Y   C1A C1A GL2
-   36   C23   C1B
-   37   H3R   C1B
-   38   H3S   C1B
-   39   C24   C1B C1B C2B
-   40   H4R   C1B C1B C2B
-   41   H4S   C1B C1B C2B
-   42   C25   C1B C2B
-   43   H5R   C1B C2B
-   44   H5S   C1B C2B
-   45   C26   C2B C2B C1B
-   46   H6R   C2B C2B C1B
-   47   H6S   C2B C2B C1B
-   48   C27   C2B
-   49   H7R   C2B
-   50   H7S   C2B
-   51   C28   C2B D3B
-   52   H8R   C2B D3B
-   53   H8S   C2B D3B
-   54   C29   D3B D3B C2B
-   55   H91   D3B
-   56  C210   D3B D3B C4B
-   57  H101   D3B
-   58  C211   C4B D3B
-   59  H11R   C4B D3B
-   60  H11S   C4B D3B
-   61  C212   C4B
-   62  H12R   C4B
-   63  H12S   C4B
-   64  C213   C4B C4B C4B C5B
-   65  H13R   C4B C4B C4B C5B
-   66  H13S   C4B C4B C4B C5B
-   67  C214   C4B C4B C5B
-   68  H14R   C4B C4B C5B
-   69  H14S   C4B C4B C5B
-   70  C215   C5B C4B
-   71  H15R   C5B C4B
-   72  H15S   C5B C4B
-   73  C216   C5B C5B C4B
-   74  H16R   C5B C5B C4B
-   75  H16S   C5B C5B C4B
-   76  C217   C5B C5B C5B C4B
-   77  H17R   C5B C5B C5B C4B
-   78  H17S   C5B C5B C5B C4B
-   79  C218   C5B
-   80  H18R   C5B
-   81  H18S   C5B
-   82  H18T   C5B
-   83   C33   C1A
-   84   H3X   C1A
-   85   H3Y   C1A
-   86   C34   C1A C1A C2A
-   87   H4X   C1A C1A C2A
-   88   H4Y   C1A C1A C2A
-   89   C35   C1A C2A
-   90   H5X   C1A C2A
-   91   H5Y   C1A C2A
-   92   C36   C2A C2A C1A
-   93   H6X   C2A C2A C1A
-   94   H6Y   C2A C2A C1A
-   95   C37   C2A 
-   96   H7X   C2A
-   97   H7Y   C2A
-   98   C38   C2A C2A C2A C3A
-   99   H8X   C2A C2A C2A C3A
-  100   H8Y   C2A C2A C2A C3A
-  101   C39   C2A C2A C3A
-  102   H9X   C2A C2A C3A
-  103   H9Y   C2A C2A C3A
-  104  C310   C3A C2A 
-  105  H10X   C3A C2A
-  106  H10Y   C3A C2A
-  107  C311   C3A C3A C2A
-  108  H11X   C3A C3A C2A
-  109  H11Y   C3A C3A C2A
-  110  C312   C3A
-  111  H12X   C3A
-  112  H12Y   C3A
-  113  C313   C3A C3A C4A
-  114  H13X   C3A C3A C4A
-  115  H13Y   C3A C3A C4A
-  116  C314   C4A C3A
-  117  H14X   C4A C3A
-  118  H14Y   C4A C3A
-  119  C315   C4A C4A C3A
-  120  H15X   C4A C4A C3A
-  121  H15Y   C4A C4A C3A
-  122  C316   C4A
-  123  H16X   C4A
-  124  H16Y   C4A
-  125  H16Z   C4A
-
-;making R stereoisomer- placing HS
-[chiral]
-HS C2 O21 C1 C3
-
-; acyl esters
-[trans]
-C22 C21 O21 C2
-[ out ]
-O22 C21 O21 C22
-[trans]
-C32 C31 O31 C3
-[out]
-O32 C31 O31 C32
-
-;cis bonds in lipind chains
-[ out ]
-H91 C29 C28 C210
-[ trans ]
-H101 C210 C29 C28
-[ out ]
-C211 C210 C29 H101
diff --git a/vermouth/data/mappings/elnedyn/popg.charmm36.map b/vermouth/data/mappings/elnedyn/popg.charmm36.map
deleted file mode 100644
index 3269bda30..000000000
--- a/vermouth/data/mappings/elnedyn/popg.charmm36.map
+++ /dev/null
@@ -1,192 +0,0 @@
-; Copyright 2018 University of Groningen
-;
-; Licensed under the Apache License, Version 2.0 (the "License");
-; you may not use this file except in compliance with the License.
-; You may obtain a copy of the License at
-;
-;    http://www.apache.org/licenses/LICENSE-2.0
-;
-; Unless required by applicable law or agreed to in writing, software
-; distributed under the License is distributed on an "AS IS" BASIS,
-; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-; See the License for the specific language governing permissions and
-; limitations under the License.
-
-; latest revision kri 15.3.2013
-[ molecule ]
-POPG
-
-[from]
-universal
-
-[to]
-elnedyn
-elnedyn22
-elnedyn22p
-
-[ martini ]
-GL0 PO4 GL1 GL2 C1A C2A C3A C4A C1B C2B D3B C4B C5B
-
-[ mapping ]
-charmm27 charmm36
-
-[ atoms ]
-    1   C13   GL0 
-    2  H13A   GL0
-    3  H13B   GL0
-    4   OC3   GL0 
-    5   HO3   GL0
-    6   C12   GL0 GL0 GL0 PO4
-    7  H12A   GL0
-    8   OC2   GL0
-    9   HO2   GL0
-   17   C11   GL0 PO4
-   18  H11A   GL0 PO4
-   19  H11B   GL0 PO4
-   20     P   PO4
-   21   O13   PO4
-   22   O14   PO4
-   23   O12   PO4 PO4 PO4 GL0
-   24   O11   PO4 PO4 GL1
-   25    C1   GL1 GL1 PO4
-   26    HA   GL1 GL1 PO4
-   27    HB   GL1 GL1 PO4
-   28    C2   GL1 GL1 GL2
-   29    HS   GL1 GL1 GL2
-   30   O21   GL1 GL1 GL2 C1B
-   31   C21   GL1 C1B
-   32   O22   GL1
-   33   C22   C1B C1B GL1 
-   34   H2R   C1B C1B GL1
-   35   H2S   C1B C1B GL1
-   36    C3   GL2 GL2 GL2 PO4
-   37    HX   GL2 GL2 GL2 PO4
-   38    HY   GL2 GL2 GL2 PO4
-   39   O31   GL2
-   40   C31   GL2 GL1 C1A
-   41   O32   GL2
-   42   C32   C1A C1A GL2
-   43   H2X   C1A C1A GL2
-   44   H2Y   C1A C1A GL2
-   45   C23   C1B
-   46   H3R   C1B
-   47   H3S   C1B
-   48   C24   C1B C1B C2B
-   49   H4R   C1B C1B C2B
-   50   H4S   C1B C1B C2B
-   51   C25   C1B C2B
-   52   H5R   C1B C2B
-   53   H5S   C1B C2B
-   54   C26   C2B C2B C1B
-   55   H6R   C2B C2B C1B
-   56   H6S   C2B C2B C1B
-   57   C27   C2B
-   58   H7R   C2B
-   59   H7S   C2B
-   60   C28   C2B D3B
-   61   H8R   C2B D3B
-   62   H8S   C2B D3B
-   63   C29   D3B D3B C2B
-   64   H91   D3B
-   65  C210   D3B D3B C4B
-   66  H101   D3B
-   67  C211   C4B D3B
-   68  H11R   C4B D3B
-   69  H11S   C4B D3B
-   70  C212   C4B
-   71  H12R   C4B
-   72  H12S   C4B
-   73  C213   C4B C4B C4B C5B
-   74  H13R   C4B C4B C4B C5B
-   75  H13S   C4B C4B C4B C5B
-   76  C214   C4B C4B C5B
-   77  H14R   C4B C4B C5B
-   78  H14S   C4B C4B C5B
-   79  C215   C5B C4B
-   80  H15R   C5B C4B
-   81  H15S   C5B C4B
-   82  C216   C5B C5B C4B
-   83  H16R   C5B C5B C4B
-   84  H16S   C5B C5B C4B
-   85  C217   C5B C5B C5B C4B
-   86  H17R   C5B C5B C5B C4B
-   87  H17S   C5B C5B C5B C4B
-   88  C218   C5B
-   89  H18R   C5B
-   90  H18S   C5B
-   91  H18T   C5B
-   92   C33   C1A
-   93   H3X   C1A
-   94   H3Y   C1A
-   95   C34   C1A C1A C2A
-   96   H4X   C1A C1A C2A
-   97   H4Y   C1A C1A C2A
-   98   C35   C1A C2A
-   99   H5X   C1A C2A
-  100   H5Y   C1A C2A
-  101   C36   C2A C2A C1A
-  102   H6X   C2A C2A C1A
-  103   H6Y   C2A C2A C1A
-  104   C37   C2A 
-  105   H7X   C2A
-  106   H7Y   C2A
-  107   C38   C2A C2A C2A C3A
-  108   H8X   C2A C2A C2A C3A
-  109   H8Y   C2A C2A C2A C3A
-  110   C39   C2A C2A C3A
-  111   H9X   C2A C2A C3A
-  112   H9Y   C2A C2A C3A
-  113  C310   C3A C2A 
-  114  H10X   C3A C2A
-  115  H10Y   C3A C2A
-  116  C311   C3A C3A C2A
-  117  H11X   C3A C3A C2A
-  118  H11Y   C3A C3A C2A
-  119  C312   C3A
-  120  H12X   C3A
-  121  H12Y   C3A
-  122  C313   C3A C3A C4A
-  123  H13X   C3A C3A C4A
-  124  H13Y   C3A C3A C4A
-  125  C314   C4A C3A
-  126  H14X   C4A C3A
-  127  H14Y   C4A C3A
-  128  C315   C4A C4A C3A
-  129  H15X   C4A C4A C3A
-  130  H15Y   C4A C4A C3A
-  131  C316   C4A
-  132  H16X   C4A
-  133  H16Y   C4A
-  134  H16Z   C4A
-
-;making R stereoisomer- placing HS
-[chiral]
-HS C2 O21 C1 C3
-
-; acyl esters
-[trans]
-C22 C21 O21 C2
-[ out ]
-O22 C21 O21 C22
-[trans]
-C32 C31 O31 C3
-[out]
-O32 C31 O31 C32
-
-;cis bonds in lipid chains
-[ out ]
-H91 C29 C28 C210
-[ trans ]
-H101 C210 C29 C28
-[ out ]
-C211 C210 C29 H101
-
-;;;making a glycerol headgroup
-[trans]
-HO3 OC3 C13 C12
-[out] 
-OC2 C12 HO3 C11
-[chiral]
-H12A C12 OC2 C13 C11
-OC2 C12 C11 C13 H12A 
-HO2 C12 C11 C13 H12A 
diff --git a/vermouth/data/mappings/elnedyn/pops.charmm36.map b/vermouth/data/mappings/elnedyn/pops.charmm36.map
deleted file mode 100644
index 237757796..000000000
--- a/vermouth/data/mappings/elnedyn/pops.charmm36.map
+++ /dev/null
@@ -1,192 +0,0 @@
-; Copyright 2018 University of Groningen
-;
-; Licensed under the Apache License, Version 2.0 (the "License");
-; you may not use this file except in compliance with the License.
-; You may obtain a copy of the License at
-;
-;    http://www.apache.org/licenses/LICENSE-2.0
-;
-; Unless required by applicable law or agreed to in writing, software
-; distributed under the License is distributed on an "AS IS" BASIS,
-; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-; See the License for the specific language governing permissions and
-; limitations under the License.
-
-[ molecule ]
-POPS
-
-[from]
-universal
-
-[to]
-elnedyn
-elnedyn22
-elnedyn22p
-
-[ martini ]
-CNO PO4 GL1 GL2 C1A C2A C3A C4A C1B C2B D3B C4B C5B
-
-[ mapping ]
-charmm27 charmm36
-
-[ atoms ]
-    1     N   CNO
-    2   HN1   CNO
-    3   HN2   CNO
-    4   HN3   CNO
-    5   C12   CNO CNO CNO PO4
-    6  H12A   CNO CNO CNO PO4
-    7   C13   CNO 
-    8  O13A   CNO
-    9  O13B   CNO
-   10   C11   PO4 CNO
-   11  H11A   PO4 CNO
-   12  H11B   PO4 CNO
-   13     P   PO4
-   14   O13   
-   15   O14   
-   16   O12   
-   17   O11   PO4 PO4 GL1
-   18    C1   GL1 GL1 PO4
-   19    HA   GL1 GL1 PO4
-   20    HB   GL1 GL1 PO4
-   21    C2   GL1 GL2
-   22    HS   GL1 GL2
-   23   O21   GL1 GL1 GL1 C1B 
-   24   C21   GL1 C1B
-   25   O22   GL1
-   26   C22   C1B C1B GL1 
-   27   H2R   C1B C1B GL1
-   28   H2S   C1B C1B GL1
-   29    C3   GL2 GL2 GL2 PO4
-   30    HX   GL2 GL2 GL2 PO4
-   31    HY   GL2 GL2 GL2 PO4
-   32   O31   GL2
-   33   C31   GL2 GL2 C1A
-   34   O32   GL2
-   35   C32   C1A C1A GL2
-   36   H2X   C1A C1A GL2
-   37   H2Y   C1A C1A GL2
-   38   C23   C1B
-   39   H3R   C1B
-   40   H3S   C1B
-   41   C24   C1B C1B C2B
-   42   H4R   C1B C1B C2B
-   43   H4S   C1B C1B C2B
-   44   C25   C1B C2B
-   45   H5R   C1B C2B
-   46   H5S   C1B C2B
-   47   C26   C2B C2B C1B
-   48   H6R   C2B C2B C1B
-   49   H6S   C2B C2B C1B
-   50   C27   C2B
-   51   H7R   C2B
-   52   H7S   C2B
-   53   C28   C2B D3B
-   54   H8R   C2B D3B
-   55   H8S   C2B D3B
-   56   C29   D3B D3B C2B
-   57   H91   D3B
-   58  C210   D3B D3B C4B
-   59  H101   D3B
-   60  C211   C4B D3B
-   61  H11R   C4B D3B
-   62  H11S   C4B D3B
-   63  C212   C4B
-   64  H12R   C4B
-   65  H12S   C4B
-   66  C213   C4B C4B C4B C5B
-   67  H13R   C4B C4B C4B C5B
-   68  H13S   C4B C4B C4B C5B
-   69  C214   C4B C4B C5B
-   70  H14R   C4B C4B C5B
-   71  H14S   C4B C4B C5B
-   72  C215   C5B C4B
-   73  H15R   C5B C4B
-   74  H15S   C5B C4B
-   75  C216   C5B C5B C4B
-   76  H16R   C5B C5B C4B
-   77  H16S   C5B C5B C4B
-   78  C217   C5B C5B C5B C4B
-   79  H17R   C5B C5B C5B C4B
-   80  H17S   C5B C5B C5B C4B
-   81  C218   C5B
-   82  H18R   C5B
-   83  H18S   C5B
-   84  H18T   C5B
-   85   C33   C1A
-   86   H3X   C1A
-   87   H3Y   C1A
-   88   C34   C1A C1A C2A
-   89   H4X   C1A C1A C2A
-   90   H4Y   C1A C1A C2A
-   91   C35   C1A C2A
-   92   H5X   C1A C2A
-   93   H5Y   C1A C2A
-   94   C36   C2A C2A C1A
-   95   H6X   C2A C2A C1A
-   96   H6Y   C2A C2A C1A
-   97   C37   C2A 
-   98   H7X   C2A
-   99   H7Y   C2A
-  100   C38   C2A C2A C2A C3A
-  101   H8X   C2A C2A C2A C3A
-  102   H8Y   C2A C2A C2A C3A
-  103   C39   C2A C2A C3A
-  104   H9X   C2A C2A C3A
-  105   H9Y   C2A C2A C3A
-  106  C310   C3A C2A 
-  107  H10X   C3A C2A
-  108  H10Y   C3A C2A
-  109  C311   C3A C3A C2A
-  110  H11X   C3A C3A C2A
-  111  H11Y   C3A C3A C2A
-  112  C312   C3A
-  113  H12X   C3A
-  114  H12Y   C3A
-  115  C313   C3A C3A C4A
-  116  H13X   C3A C3A C4A
-  117  H13Y   C3A C3A C4A
-  118  C314   C4A C3A
-  119  H14X   C4A C3A
-  120  H14Y   C4A C3A
-  121  C315   C4A C4A C3A
-  122  H15X   C4A C4A C3A
-  123  H15Y   C4A C4A C3A
-  124  C316   C4A
-  125  H16X   C4A
-  126  H16Y   C4A
-  127  H16Z   C4A
-
-; making 
-[out]
- C13  N C3 C11
-[chiral]
- H12A C12 N C11 C13
-[chiral]
- C13 C12 H12A C11 N 
- O13A C12 H12A C11 N
- O13B C12 H12A C11 N
-
-
-;making R stereoisomer- placing HS
-[chiral]
-HS C2 O21 C1 C3
-
-; acyl esters
-[trans]
-C22 C21 O21 C2
-[ out ]
-O22 C21 O21 C22
-[trans]
-C32 C31 O31 C3
-[out]
-O32 C31 O31 C32
-
-;cis bonds in lipind chains
-[ out ]
-H9R C29 C28 C210
-[ trans ]
-H10R C210 C29 C28
-[ out ]
-C211 C210 C29 H10R
diff --git a/vermouth/data/mappings/elnedyn/pro.charmm36.map b/vermouth/data/mappings/elnedyn/pro.charmm36.map
old mode 100755
new mode 100644
index 587c3170a..7e5e68dcd
--- a/vermouth/data/mappings/elnedyn/pro.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/pro.charmm36.map
@@ -19,7 +19,7 @@ PRO
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 elnedyn22p
 
diff --git a/vermouth/data/mappings/elnedyn/ser.charmm36.map b/vermouth/data/mappings/elnedyn/ser.charmm36.map
old mode 100755
new mode 100644
index 37c2c7dc5..400ea6b50
--- a/vermouth/data/mappings/elnedyn/ser.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/ser.charmm36.map
@@ -19,7 +19,7 @@ SER
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 
 [ martini ]
diff --git a/vermouth/data/mappings/elnedyn/thr.charmm36.map b/vermouth/data/mappings/elnedyn/thr.charmm36.map
index 748a748ce..3aed3bc22 100644
--- a/vermouth/data/mappings/elnedyn/thr.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/thr.charmm36.map
@@ -22,7 +22,7 @@ BB SC1
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 
 [ mapping ]
diff --git a/vermouth/data/mappings/elnedyn/trp.charmm36.map b/vermouth/data/mappings/elnedyn/trp.charmm36.map
index 6726eacf0..f0a3c4e68 100644
--- a/vermouth/data/mappings/elnedyn/trp.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/trp.charmm36.map
@@ -19,7 +19,7 @@ TRP
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 elnedyn22p
 
diff --git a/vermouth/data/mappings/elnedyn/tyr.charmm36.map b/vermouth/data/mappings/elnedyn/tyr.charmm36.map
index 865f4b366..a7a444533 100644
--- a/vermouth/data/mappings/elnedyn/tyr.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/tyr.charmm36.map
@@ -19,7 +19,7 @@ TYR
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 elnedyn22p
 
diff --git a/vermouth/data/mappings/elnedyn/val.charmm36.map b/vermouth/data/mappings/elnedyn/val.charmm36.map
index 8fa19163d..78ba6bda0 100644
--- a/vermouth/data/mappings/elnedyn/val.charmm36.map
+++ b/vermouth/data/mappings/elnedyn/val.charmm36.map
@@ -19,7 +19,7 @@ VAL
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 elnedyn22p
 
@@ -37,4 +37,4 @@ charmm27 charmm36
     8   CG1   SC1 
    12   CG2   SC1
    16    C    !BB
-   17    O    !BB
\ No newline at end of file
+   17    O    !BB
diff --git a/vermouth/data/mappings/elnedyn21/ala.charmm36.map b/vermouth/data/mappings/elnedyn21/ala.charmm36.map
new file mode 100644
index 000000000..b65dbc71b
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/ala.charmm36.map
@@ -0,0 +1,48 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+ALA
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+elnedyn22p
+
+[ martini ]
+BB
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    5    CB    !BB
+    9    C    !BB
+   10    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+  HB3    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Ala
+; HA     CA    N    C    CB ; D-Ala
diff --git a/vermouth/data/mappings/elnedyn21/arg.charmm36.elnedyn22p.map b/vermouth/data/mappings/elnedyn21/arg.charmm36.elnedyn22p.map
new file mode 100644
index 000000000..ac5461162
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/arg.charmm36.elnedyn22p.map
@@ -0,0 +1,76 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+ARG
+
+[from]
+universal
+
+[to]
+elnedyn22p
+
+[ martini ]
+BB SC1 SC2
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    5    CB   SC1
+    8    CG   SC1
+   11    CD   SC1 
+   14    NE   SC2
+   15    HE   SC2
+   16    CZ   SC2
+   17   NH1   SC2
+   18  HH11   SC2
+   19  HH12   SC2
+   20   NH2   SC2
+   21  HH21   SC2
+   22  HH22   SC2
+   23    C    !BB
+   24    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+[ chiral ]
+  HA     CA    N    CB    C ; L-Arg
+; HA     CA    N    C    CB ; D-Arg
+
+
+; The cis/trans are added to ensure proper
+; splitting of the guanidinium group
+
+[ trans ]
+; Because of the use of normalized vectors, this makes sense:
+  NH1    CZ    NE    HE
+
+[ out ]
+  NH2    CZ    NE    NH1
+  NH1    CZ    NE    NH2
+
+[ out ]
+ HH11    NH1   CZ   HH12
+ HH12    NH1   CZ   HH11
+ HH21    NH2   CZ   HH22
+ HH22    NH2   CZ   HH21
+
+[ extra ]
+SCP
diff --git a/vermouth/data/mappings/elnedyn21/arg.charmm36.map b/vermouth/data/mappings/elnedyn21/arg.charmm36.map
new file mode 100644
index 000000000..aaa99ffad
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/arg.charmm36.map
@@ -0,0 +1,74 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+ARG
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+
+[ martini ]
+BB SC1 SC2
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    5    CB   SC1
+    8    CG   SC1
+   11    CD   SC1 
+   14    NE   SC2
+   15    HE   SC2
+   16    CZ   SC2
+   17   NH1   SC2
+   18  HH11   SC2
+   19  HH12   SC2
+   20   NH2   SC2
+   21  HH21   SC2
+   22  HH22   SC2
+   23    C    !BB
+   24    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+[ chiral ]
+  HA     CA    N    CB    C ; L-Arg
+; HA     CA    N    C    CB ; D-Arg
+
+
+; The cis/trans are added to ensure proper
+; splitting of the guanidinium group
+
+[ trans ]
+; Because of the use of normalized vectors, this makes sense:
+  NH1    CZ    NE    HE
+
+[ out ]
+  NH2    CZ    NE    NH1
+  NH1    CZ    NE    NH2
+
+[ out ]
+ HH11    NH1   CZ   HH12
+ HH12    NH1   CZ   HH11
+ HH21    NH2   CZ   HH22
+ HH22    NH2   CZ   HH21
diff --git a/vermouth/data/mappings/elnedyn21/asn.charmm36.elnedyn22p.map b/vermouth/data/mappings/elnedyn21/asn.charmm36.elnedyn22p.map
new file mode 100644
index 000000000..be748bd8e
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/asn.charmm36.elnedyn22p.map
@@ -0,0 +1,56 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+ASN
+
+[from]
+universal
+
+[to]
+elnedyn22p
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+;    4    HA    BB
+    5    CB   SC1
+;    6   HB1   SC1
+;    7   HB2   SC1
+    8    CG   SC1
+    9   OD1   SC1
+   10   ND2   SC1
+   11  HD21   SC1
+   12  HD22   SC1
+   13    C    !BB
+   14    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Asn
+; HA     CA    N    C    CB ; D-Asn
+
+[ extra ]
+SCP SCN
diff --git a/vermouth/data/mappings/elnedyn21/asn.charmm36.map b/vermouth/data/mappings/elnedyn21/asn.charmm36.map
new file mode 100644
index 000000000..dad8d4f45
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/asn.charmm36.map
@@ -0,0 +1,54 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+ASN
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+;    4    HA    BB
+    5    CB   SC1
+;    6   HB1   SC1
+;    7   HB2   SC1
+    8    CG   SC1
+    9   OD1   SC1
+   10   ND2   SC1
+   11  HD21   SC1
+   12  HD22   SC1
+   13    C    !BB
+   14    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Asn
+; HA     CA    N    C    CB ; D-Asn
diff --git a/vermouth/data/mappings/elnedyn21/asp.charmm36.elnedyn22p.map b/vermouth/data/mappings/elnedyn21/asp.charmm36.elnedyn22p.map
new file mode 100644
index 000000000..690f64953
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/asp.charmm36.elnedyn22p.map
@@ -0,0 +1,55 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+ASP
+
+[from]
+universal
+
+[to]
+elnedyn22p
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+;    4    HA    BB
+    5    CB   SC1
+;    6   HB1   SC1
+;    7   HB2   SC1
+    8    CG   SC1
+    9   OD1   SC1
+   10   OD2   SC1
+;   11   HD2   SC1
+   12    C    !BB
+   13    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Asp
+; HA     CA    N    C    CB ; D-Asp
+
+[ extra ]
+SCN
diff --git a/vermouth/data/mappings/elnedyn21/asp.charmm36.map b/vermouth/data/mappings/elnedyn21/asp.charmm36.map
new file mode 100644
index 000000000..19aab52aa
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/asp.charmm36.map
@@ -0,0 +1,53 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+ASP
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+;    4    HA    BB
+    5    CB   SC1
+;    6   HB1   SC1
+;    7   HB2   SC1
+    8    CG   SC1
+    9   OD1   SC1
+   10   OD2   SC1
+;   11   HD2   SC1
+   12    C    !BB
+   13    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Asp
+; HA     CA    N    C    CB ; D-Asp
diff --git a/vermouth/data/mappings/elnedyn21/cys.charmm36.map b/vermouth/data/mappings/elnedyn21/cys.charmm36.map
new file mode 100644
index 000000000..3904d4525
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/cys.charmm36.map
@@ -0,0 +1,48 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+CYS
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+elnedyn22p
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    4    CB   SC1
+    7    SG   SC1
+    9    C    !BB
+   10    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Cys
+; HA     CA    N    C    CB ; D-Cys
diff --git a/vermouth/data/mappings/elnedyn21/gln.charmm36.elnedyn22p.map b/vermouth/data/mappings/elnedyn21/gln.charmm36.elnedyn22p.map
new file mode 100644
index 000000000..f7cb9fd9e
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/gln.charmm36.elnedyn22p.map
@@ -0,0 +1,56 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+GLN
+
+[from]
+universal
+
+[to]
+elnedyn22p
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    4    CB   SC1
+    5    CG   SC1
+    6    CD   SC1 
+    7   OE1   SC1
+    8   NE2   SC1
+    9  HE21   SC1
+   10  HE22   SC1
+   11  HE11   SC1
+   12  HE12   SC1
+   13    C    !BB
+   14    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Gln
+; HA     CA    N    C    CB ; D-Gln
+
+[ extra ]
+SCP SCN
diff --git a/vermouth/data/mappings/elnedyn21/gln.charmm36.map b/vermouth/data/mappings/elnedyn21/gln.charmm36.map
new file mode 100644
index 000000000..36916484d
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/gln.charmm36.map
@@ -0,0 +1,54 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+GLN
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    4    CB   SC1
+    5    CG   SC1
+    6    CD   SC1 
+    7   OE1   SC1
+    8   NE2   SC1
+    9  HE21   SC1
+   10  HE22   SC1
+   11  HE11   SC1
+   12  HE12   SC1
+   13    C    !BB
+   14    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Gln
+; HA     CA    N    C    CB ; D-Gln
diff --git a/vermouth/data/mappings/elnedyn21/glu.charmm36.elnedyn22p.map b/vermouth/data/mappings/elnedyn21/glu.charmm36.elnedyn22p.map
new file mode 100644
index 000000000..c9b357e3b
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/glu.charmm36.elnedyn22p.map
@@ -0,0 +1,58 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+GLU
+
+[from]
+universal
+
+[to]
+elnedyn22p
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+;    4    HA    BB
+    5    CB   SC1
+;    6   HB1   SC1
+;    7   HB2   SC1
+    8    CG   SC1
+;    9   HG1   SC1
+;   10   HG2   SC1
+   11    CD   SC1
+   12   OE1   SC1
+   13   OE2   SC1
+;   14   HE2   SC1
+   15    C    !BB
+   16    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Glu
+; HA     CA    N    C    CB ; D-Glu
+
+[ extra ]
+SCN
diff --git a/vermouth/data/mappings/elnedyn21/glu.charmm36.map b/vermouth/data/mappings/elnedyn21/glu.charmm36.map
new file mode 100644
index 000000000..f79c56276
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/glu.charmm36.map
@@ -0,0 +1,56 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+GLU
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+;    4    HA    BB
+    5    CB   SC1
+;    6   HB1   SC1
+;    7   HB2   SC1
+    8    CG   SC1
+;    9   HG1   SC1
+;   10   HG2   SC1
+   11    CD   SC1
+   12   OE1   SC1
+   13   OE2   SC1
+;   14   HE2   SC1
+   15    C    !BB
+   16    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Glu
+; HA     CA    N    C    CB ; D-Glu
diff --git a/vermouth/data/mappings/elnedyn21/gly.charmm36.map b/vermouth/data/mappings/elnedyn21/gly.charmm36.map
new file mode 100644
index 000000000..3ac6ed796
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/gly.charmm36.map
@@ -0,0 +1,37 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+GLY
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+elnedyn22p
+
+[ martini ]
+BB
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    9    C    !BB
+   10    O    !BB
diff --git a/vermouth/data/mappings/elnedyn21/his.charmm36.map b/vermouth/data/mappings/elnedyn21/his.charmm36.map
new file mode 100644
index 000000000..5ad2aabff
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/his.charmm36.map
@@ -0,0 +1,61 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+HIS  ;;;; is in fact HSP but if one of hydrogen on a nitrogen is missing in the input topology file, will become HSE or HSD automatically
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+elnedyn22p
+
+[ martini ]
+BB SC1 SC2 SC3
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    5    CB   SC1
+    8   CD2   SC2
+    9   HD2   SC2
+   10    CG   SC1
+   11   NE2   SC2
+   12   HE2   SC2
+   13   ND1   SC3
+   14   HD1   SC3
+   15   CE1   SC3
+   16   HE1   SC3
+   17    C    !BB
+   18    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-His
+; HA     CA    N    C    CB ; D-His
+
+[out]
+HD1 ND1 CG NE2
+HD2 CD2 CE1 CG
+HE2 NE2 CE1 CD2
diff --git a/vermouth/data/mappings/elnedyn21/ile.charmm36.map b/vermouth/data/mappings/elnedyn21/ile.charmm36.map
new file mode 100644
index 000000000..f165065e4
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/ile.charmm36.map
@@ -0,0 +1,70 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+ILE
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+elnedyn22p
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+;    4    HA    BB
+    5    CB   SC1
+;    6    HB   SC1
+    7   CG2   SC1
+;    8  HG21   SC1
+;    9  HG22   SC1
+;   10  HG23   SC1
+   11   CG1   SC1
+;   12  HG11   SC1
+;   13  HG12   SC1
+   14    CD   SC1
+;   15   HD1   SC1
+;   16   HD2   SC1
+;   17   HD3   SC1
+   18    C    !BB
+   19    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Ile
+; HA     CA    N    C    CB ; D-Ile
+
+[ out ]
+CG2 CB CG1 CA
+HG21 CB CG1 CA
+HG22 CB CG1 CA
+HG23 CB CG1 CA
+
+[ chiral ]
+  HB     CB    CA   CG2   CG1  ; 3S stereoisomer (natural form)
+; HB     CB    CA   CG1   CG2  ; 3R stereoisomer
diff --git a/vermouth/data/mappings/elnedyn21/leu.charmm36.map b/vermouth/data/mappings/elnedyn21/leu.charmm36.map
new file mode 100644
index 000000000..690254085
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/leu.charmm36.map
@@ -0,0 +1,56 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+LEU
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+elnedyn22p
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    5    CB   SC1
+    8    CG   SC1
+   10   CD1   SC1
+   14   CD2   SC1
+   18    C    !BB
+   19    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Leu
+; HA     CA    N    C    CB ; D-Leu
+
+[ out ] 
+CD2  CG CD1 CB
+HD21 CG CD1 CB
+HD22 CG CD1 CB
+HD23 CG CD1 CB
diff --git a/vermouth/data/mappings/elnedyn21/lys.charmm36.elnedyn22p.map b/vermouth/data/mappings/elnedyn21/lys.charmm36.elnedyn22p.map
new file mode 100644
index 000000000..02632256e
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/lys.charmm36.elnedyn22p.map
@@ -0,0 +1,64 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+LYS
+
+[from]
+universal
+
+[to]
+elnedyn22p
+
+[ martini ]
+BB SC1 SC2
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+;    4    HA    BB
+    5    CB   SC1
+;    6   HB1   SC1
+;    7   HB2   SC1
+    8    CG   SC1
+;    9   HG1   SC1
+;   10   HG2   SC1
+   11    CD   SC1
+;   12   HD1   SC1
+;   13   HD2   SC1
+   14    CE   SC2
+;   15   HE1   SC2
+;   16   HE2   SC2
+   17    NZ   SC2
+   18   HZ1   SC2
+   19   HZ2   SC2
+   20   HZ3   SC2
+   21    C    !BB
+   22    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Lys
+; HA     CA    N    C    CB ; D-Lys
+
+[ extra ]
+SCP
diff --git a/vermouth/data/mappings/elnedyn21/lys.charmm36.map b/vermouth/data/mappings/elnedyn21/lys.charmm36.map
new file mode 100644
index 000000000..f728eefae
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/lys.charmm36.map
@@ -0,0 +1,62 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+LYS
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+
+[ martini ]
+BB SC1 SC2
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+;    4    HA    BB
+    5    CB   SC1
+;    6   HB1   SC1
+;    7   HB2   SC1
+    8    CG   SC1
+;    9   HG1   SC1
+;   10   HG2   SC1
+   11    CD   SC1
+;   12   HD1   SC1
+;   13   HD2   SC1
+   14    CE   SC2
+;   15   HE1   SC2
+;   16   HE2   SC2
+   17    NZ   SC2
+   18   HZ1   SC2
+   19   HZ2   SC2
+   20   HZ3   SC2
+   21    C    !BB
+   22    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Lys
+; HA     CA    N    C    CB ; D-Lys
diff --git a/vermouth/data/mappings/elnedyn21/met.charmm36.map b/vermouth/data/mappings/elnedyn21/met.charmm36.map
new file mode 100644
index 000000000..f9685a7df
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/met.charmm36.map
@@ -0,0 +1,58 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+MET
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+elnedyn22p
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+;    4    HA    BB
+    5    CB   SC1
+;    6   HB1   SC1
+;    7   HB2   SC1
+    8    CG   SC1
+;    9   HG1   SC1
+;   10   HG2   SC1
+   11    SD   SC1
+   12    CE   SC1
+;   13   HE1   SC1
+;   14   HE2   SC1
+;   15   HE3   SC1
+   16    C    !BB
+   17    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Met
+; HA     CA    N    C    CB ; D-Met
diff --git a/vermouth/data/mappings/elnedyn/modifications.mapping b/vermouth/data/mappings/elnedyn21/modifications.mapping
similarity index 95%
rename from vermouth/data/mappings/elnedyn/modifications.mapping
rename to vermouth/data/mappings/elnedyn21/modifications.mapping
index 53b78c92c..6799b7d87 100644
--- a/vermouth/data/mappings/elnedyn/modifications.mapping
+++ b/vermouth/data/mappings/elnedyn21/modifications.mapping
@@ -2,7 +2,7 @@
 [ from ]
 universal
 [ to ]
-elnedyn
+elnedyn21
 
 [ from blocks ]
 C-ter
@@ -28,7 +28,7 @@ OXT BB 0
 [ from ]
 universal
 [ to ]
-elnedyn
+elnedyn21
 [ from blocks ]
 N-ter
 [ to blocks ]
@@ -54,7 +54,7 @@ O   BB 0
 [ from ]
 universal
 [ to ]
-elnedyn
+elnedyn21
 
 [ from blocks ]
 COOH-ter
@@ -83,7 +83,7 @@ OXT BB 0
 [ from ]
 universal
 [ to ]
-elnedyn
+elnedyn21
 [ from blocks ]
 NH2-ter
 [ to blocks ]
diff --git a/vermouth/data/mappings/elnedyn21/phe.charmm36.map b/vermouth/data/mappings/elnedyn21/phe.charmm36.map
new file mode 100644
index 000000000..8ffd2a4f1
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/phe.charmm36.map
@@ -0,0 +1,82 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+PHE
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+elnedyn22p
+
+[ martini ]
+BB SC1 SC2 SC3
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+;    4    HA    BB
+    5    CB   SC1
+;    6   HB1   SC1
+;    7   HB2   SC1
+    8    CG   SC1
+    9   CD1   SC1
+   10   HD1   SC1
+   11   CE1   SC3
+   12   HE1   SC3
+   13    CZ   SC3
+   14    HZ   SC3
+   15   CD2   SC2
+   16   HD2   SC2 
+   17   CE2   SC2
+   18   HE2   SC2
+   19    C    !BB
+   20    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Phe
+; HA     CA    N    C    CB ; D-Phe
+
+
+[ out ]
+; Add some helper points
+P CD1 CD2 CZ
+Q CD2 CD1 CZ
+R CZ  CD1 CD2
+
+[ trans ]
+; Place hydrogens using helper points
+HD1   P CE1   R
+HD2   Q CE2   R
+HE1 CE1   P  CG
+HE2 CE2   Q  CG
+HZ    R CE1   P 
+
+[ out ]
+; Place ring carbons
+CD1 CE1 HE1 R
+CD2 CE2 HE2 R
+CZ  CE1 HE1 P
diff --git a/vermouth/data/mappings/elnedyn21/pro.charmm36.map b/vermouth/data/mappings/elnedyn21/pro.charmm36.map
new file mode 100644
index 000000000..7e5e68dcd
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/pro.charmm36.map
@@ -0,0 +1,48 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+PRO
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+elnedyn22p
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    CD   SC1
+    3    CA    BB
+    4    CB   SC1
+    5    CG   SC1
+    6    C    !BB
+    7    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Pro
+; HA     CA    N    C    CB ; D-Pro
diff --git a/vermouth/data/mappings/elnedyn21/ser.charmm36.elnedyn22p.map b/vermouth/data/mappings/elnedyn21/ser.charmm36.elnedyn22p.map
new file mode 100644
index 000000000..b958e986d
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/ser.charmm36.elnedyn22p.map
@@ -0,0 +1,50 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+SER
+
+[from]
+universal
+
+[to]
+elnedyn22p
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    5    CB   SC1
+    8    OG   SC1
+    9   HG1   SC1
+   10    C    !BB
+   11    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Ser
+; HA     CA    N    C    CB ; D-Ser
+
+[ extra ]
+SCP SCN
diff --git a/vermouth/data/mappings/elnedyn21/ser.charmm36.map b/vermouth/data/mappings/elnedyn21/ser.charmm36.map
new file mode 100644
index 000000000..400ea6b50
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/ser.charmm36.map
@@ -0,0 +1,48 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+SER
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    5    CB   SC1
+    8    OG   SC1
+    9   HG1   SC1
+   10    C    !BB
+   11    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Ser
+; HA     CA    N    C    CB ; D-Ser
diff --git a/vermouth/data/mappings/elnedyn21/thr.charmm36.elnedyn22p.map b/vermouth/data/mappings/elnedyn21/thr.charmm36.elnedyn22p.map
new file mode 100644
index 000000000..cebd99544
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/thr.charmm36.elnedyn22p.map
@@ -0,0 +1,59 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+THR
+
+[from]
+universal
+
+[to]
+elnedyn22p
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    5    CB   SC1
+    7   OG1   SC1
+    8   HG1   SC1
+    9   CG2   SC1 
+   13    C    !BB
+   14    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB     CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Thr
+; HA     CA    N    C    CB ; D-Thr
+
+[ out ] 
+OG1 CB CG2 CA
+[ trans ]
+HG1 OG1 CB CA
+
+[ chiral ]
+  HB  CB  CG2  OG1 CA  ; 3R stereoisomer (natural form)
+; HB  CB  CG2  CA  CG1 ; 3S stereoisomer
+
+[ extra ]
+SCP SCN
diff --git a/vermouth/data/mappings/elnedyn21/thr.charmm36.map b/vermouth/data/mappings/elnedyn21/thr.charmm36.map
new file mode 100644
index 000000000..3aed3bc22
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/thr.charmm36.map
@@ -0,0 +1,57 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+THR
+
+[ martini ]
+BB SC1
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    5    CB   SC1
+    7   OG1   SC1
+    8   HG1   SC1
+    9   CG2   SC1 
+   13    C    !BB
+   14    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB     CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Thr
+; HA     CA    N    C    CB ; D-Thr
+
+[ out ] 
+OG1 CB CG2 CA
+[ trans ]
+HG1 OG1 CB CA
+
+[ chiral ]
+  HB  CB  CG2  OG1 CA  ; 3R stereoisomer (natural form)
+; HB  CB  CG2  CA  CG1 ; 3S stereoisomer
diff --git a/vermouth/data/mappings/elnedyn21/trp.charmm36.map b/vermouth/data/mappings/elnedyn21/trp.charmm36.map
new file mode 100644
index 000000000..f0a3c4e68
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/trp.charmm36.map
@@ -0,0 +1,71 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+TRP
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+elnedyn22p
+
+[ martini ]
+BB SC1 SC2 SC3 SC4
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    5    CB   SC1
+    8    CG   SC1
+    9   CD1   SC2 
+   10   HD1   SC2
+   11   NE1   SC2
+   12   HE1   SC2
+   13   CE2   SC2
+   14   CD2   SC1
+   15   CE3   SC3
+   16   HE3   SC3
+   17   CZ3   SC3
+   18   HZ3   SC3 
+   19   CZ2   SC4
+   20   HZ2   SC4 
+   21   CH2   SC4
+   22   HH2   SC4
+   23    C    !BB
+   24    O    !BB
+
+[ trans ]
+CB  CG  CD2 CE2  
+HD1 CD1 NE1 CE2
+HE1 NE1 CD1 CG
+HE3 CE3 CD2 CE2
+HZ2 CZ2 CE2 CD2
+HZ3 CZ3 CE3 CD2
+HH2 CH2 CZ3 CE3
+
+[ chiral ]
+  CB     CA    N    C  
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Trp
+; HA     CA    N    C    CB ; D-Trp
diff --git a/vermouth/data/mappings/elnedyn21/tyr.charmm36.map b/vermouth/data/mappings/elnedyn21/tyr.charmm36.map
new file mode 100644
index 000000000..a7a444533
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/tyr.charmm36.map
@@ -0,0 +1,80 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+TYR
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+elnedyn22p
+
+[ martini ]
+BB SC1 SC2 SC3
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    5    CB   SC1
+    8    CG   SC1
+    9   CD1   SC1
+   10   HD1   SC1
+   11   CE1   SC3
+   12   HE1   SC3
+   13    CZ   SC3
+   14    OH   SC3
+   15    HH   SC3
+   16   CD2   SC2
+   17   HD2   SC2
+   18   CE2   SC2
+   19   HE2   SC2
+   20    C    !BB
+   21    O    !BB
+
+[ chiral ]
+  CB     CA    N    C
+  HB1    CA    N    C
+  HB2    CA    N    C
+
+[ chiral ]
+  HA     CA    N    CB    C ; L-Tyr
+; HA     CA    N    C    CB ; D-Tyr
+
+[ out ]
+; Add some helper points
+P CD1 CD2 CZ
+Q CD2 CD1 CZ
+R CZ  CD1 CD2
+
+[ trans ]
+; Place hydrogens using helper points
+HD1   P CE1   R
+HD2   Q CE2   R
+HE1 CE1   P  CG
+HE2 CE2   Q  CG
+OH    R CE1   P
+HH   OH   R CE1 
+
+[ out ]
+; Place ring carbons
+CD1 CE1 HE1 R
+CD2 CE2 HE2 R
+CZ  CE1 HE1 P
diff --git a/vermouth/data/mappings/elnedyn21/val.charmm36.map b/vermouth/data/mappings/elnedyn21/val.charmm36.map
new file mode 100644
index 000000000..78ba6bda0
--- /dev/null
+++ b/vermouth/data/mappings/elnedyn21/val.charmm36.map
@@ -0,0 +1,40 @@
+; Copyright 2018 University of Groningen
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;    http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[ molecule ]
+VAL
+
+[from]
+universal
+
+[to]
+elnedyn21
+elnedyn22
+elnedyn22p
+
+[ martini ]
+BB SC1
+
+[ mapping ]
+charmm27 charmm36
+
+[ atoms ]
+    1     N    !BB
+    2    HN    !BB
+    3    CA    BB
+    5    CB   SC1
+    8   CG1   SC1 
+   12   CG2   SC1
+   16    C    !BB
+   17    O    !BB


Test patch:
diff --git a/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/command b/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/command
index 0e6cef4cc..3410e70ed 100644
--- a/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/command
+++ b/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/command
@@ -2,7 +2,7 @@ martinize2
 -f ../aa.pdb
 -x cg.pdb
 -o topol.top
--ff elnedyn
+-ff elnedyn21
 -ss CCSHHHHHHHHHHCCCCHHHHHHHHHHHTSCHHHHHHHTCCCC
 -nter NH2-ter
 -cter COOH-ter
diff --git a/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/molecule_0.itp b/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/molecule_0.itp
index 5df549859..109956d11 100644
--- a/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/molecule_0.itp
+++ b/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/molecule_0.itp
@@ -52,7 +52,7 @@ molecule_0 1
 41 P5  17 ASN BB  41  0.0 
 42 P5  17 ASN SC1 42  0.0 
 43 N0  18 PRO BB  43  0.0 
-44 C2  18 PRO SC1 44  0.0 
+44 AC2 18 PRO SC1 44  0.0 
 45 Nd  19 GLU BB  45  0.0 
 46 Qa  19 GLU SC1 46 -1.0 
 47 Nd  20 GLU BB  47  0.0 
diff --git a/vermouth/tests/test_redistributed_kdtree.py b/vermouth/tests/test_redistributed_kdtree.py
index 30648b0d2..092fe0071 100644
--- a/vermouth/tests/test_redistributed_kdtree.py
+++ b/vermouth/tests/test_redistributed_kdtree.py
@@ -33,31 +33,14 @@
     HAS_SCIPY = True
 
 
-def dict_close(left, right):
-    """
-    Compare 2 dicts whith floats as values.
-
-    Returns `True` is all the keys are the same and the values are all close
-    according to :func:`np.allclose`.
-
-    The order of the keys is not kept.
-    """
-    if left.keys() != right.keys():
-        return False
-    keys = sorted(left)
-    values_left = np.array([left[key] for key in keys])
-    values_right = np.array([right[key] for key in keys])
-    return np.allclose(values_left, values_right)
-
-
 @pytest.mark.skipif(not HAS_SCIPY, reason="Scipy is not available.")
 @hypothesis.given(
     coordinates=hnp.arrays(
         dtype=st.sampled_from((np.float32, np.float64)),
-        shape=st.tuples(st.integers(1, 10), st.integers(1, 10)),
+        shape=st.tuples(st.integers(2, 10), st.integers(2, 10)),
         elements=st.floats(allow_nan=False, allow_infinity=False, width=32),
     ),
-    max_dist=st.floats(0, 5, width=32),
+    max_dist=st.floats(1e-3, 5),
     p=st.integers(1, 5),
 )
 def test_sparse_distance_matrix(coordinates, max_dist, p):
@@ -65,10 +48,11 @@ def test_sparse_distance_matrix(coordinates, max_dist, p):
     Test that the `sparse_distance_matrix` method returns the same thing in the
     redistributed KDTree and on the actual scipy one.
     """
+
     original_tree = scipyKDTree(coordinates)
     redis_tree = redisKDTree(coordinates)
 
     original_output = original_tree.sparse_distance_matrix(original_tree, max_dist, p)
+    hypothesis.assume(original_output.count_nonzero())
     redis_output = redis_tree.sparse_distance_matrix(redis_tree, max_dist, p)
-
-    assert dict_close(redis_output, original_output)
+    assert redis_output == pytest.approx(original_output)
diff --git a/vermouth/tests/test_utils.py b/vermouth/tests/test_utils.py
index 52e734473..a6a474dca 100644
--- a/vermouth/tests/test_utils.py
+++ b/vermouth/tests/test_utils.py
@@ -188,7 +188,7 @@ def test_distance(vec_and_dist):
     Test the results of :func:`utils.distance`.
     """
     point1, point2, distance = vec_and_dist
-    assert_allclose(utils.distance(point1, point2), distance)
+    assert_allclose(utils.distance(point1, point2), distance, atol=1e-8)
 
 
 @pytest.mark.parametrize(