***** Facio's Release History *****----- Ver.24.1.2 ----- September 13, 2022
Default of FMO/ESP was changed to "Standard"----- Ver.24.1.1 ----- September 5, 2022

GUI for FMO 5.5
Box Drawer----- Ver.23.1.5 ----- July 14, 2021
bug fixed----- Ver.23.1.4 ----- July 1, 2021
Tetrahedron Drawer has been implemented. See at Tools menu. This utility can draw translucent
tetrahedron with vertices at specified atoms, as shown below.

----- Ver.23.1.3 --------- Ver.23.1.2 --------- Ver.23.1.1 --------- Ver.22.1.1 --------- Ver.21.2.1 --------- Ver.21.1.1 -----

October 16, 2020 bug fixed
October 12, 2020 Revision of GUI for FMO 5.4 for 32bit version and bug fix
October 5, 2020 Revision of GUI for FMO 5.4 and bug fix
December 25, 2018 Revision of GUI for FMO 5.3 and bug fix
October 19, 2018bug fixed
April 24, 2018
64bit version released and bug fixed----- Ver.20.1.3 ----- September 12, 2017bug fixed----- Ver.20.1.2 ----- August 17, 2017bug fixed----- Ver.20.1.1 ----- August 12, 2017
Revision of GUI for FMO

----- Ver.19.2.1 ----- July 23, 2016
Revision of the function “Find Neighboring Fragments” in FMO menu.
Reference fragment

Range that defines “neighboring fragments

Reference fragment
within 5-10 Angstroms

within 10-15 Angstroms

within 15-20 Angstroms

----- Ver.19.1.7 --------- Ver.19.1.6 --------- Ver.19.1.5 --------- Ver.19.1.4 --------- Ver.19.1.3 --------- Ver.19.1.2 --------- Ver.19.1.1 -----

May 25, 2016 Minor bug fix for MOPAC2016 ver.16
February 17, 2016 Bug fix for Summarize Energy/Grad/Geometry Change
February 3, 2016 Bug fix for Summarize Energy/Grad/Geometry Change
July 18, 2015
Minor bug fix for NMR Shielding Tensor reading
April 23, 2015 For two different output formats of MOPAC 6.06
April 9, 2015
Minor bug fix for MOPAC2012 ver.15
April 4, 2015

The behavior of Facio on Mac OS X or Ubuntu Linux, especially in executing external programs(such as, Tinker, MSMS, MOPAC, Firefly and Gamess) as Facio’s child process, has been fully
examined and revised.
For Tinker, MSMS, MOPAC2012, please use Windows executable even if on Mac OS X or Linux
environment. For Firefly or Gamess (US), see below.
Wineskin App version of Facio is now available for Mac OS X.

Wineskin App
of Facio

If you want to use Facio on Ubuntu Linux, be sure to install wine by typing “sudo apt-get installwine” and set Facio to Linux-WINE mode. On Ubuntu Linux, both Windows and Linux versionof Firefly can be used with Facio as in Windows environment. For Gamess (US), only Linux
executable can be used.

----- Ver.18.8.2 ----- October 24, 2014 Bug about reading MOPAC2012 Ver.14 calculations of 1
atom and 2 atoms molecule was fixed.
----- Ver.18.8.1 ----- August 14, 2014 Bug in the routine which finds bonds to isolated hydrogen
atom was fixed. This bug has influenced possibly to FMO fragmentation since ver. 16.1.1.
----- Ver.18.7.4 ----- July 26, 2014 Bug about Gamess’s current directory fixed----- Ver.18.7.3 ----- July 1, 2014
$DATA record of FMO input file was incomplete in Facio 18.6.1 to 18.7.2. Bug fixed.
----- Ver.18.7.2 ----- June 28, 2014
Minor modification to the function of recording Gaussian’s current directory----- Ver.18.7.1 -----

June 16, 2014(1) IRC Viewer has been fully revised. Each structure at respective IRC point is saved as PDB in
the PDB¥IRCResults in Facio’s root folder. With this change, bonds are properly displayed ateach IRC point as shown below.

Transition State(2) Output format of MOPAC2012 Ver.14 and Ver.13 are slightly different in the part of Cartesian
Coordinate. Facio is now compatible with both version.
(3) %NProc in Gaussian Link 0 has been changed to %NProcShared.
(4) Current directory for the respective PDB, Gamess, Gaussian and Gaussian formatted checkfiles are now saved in CurrDir.ini in the Facio’s root folder. This function will be useful when
you change folder to save or read these files.

----- Ver.18.6.2 ----- April 12, 2014
Bug related to the execution of Tinker/newton.exe was fixed.
----- Ver.18.6.1 ----- April 5, 2014
Function to generate atom type and partial charge data for Gaussian/AMBER calculation fromprotein PDB file has been implemented.
-N3-0.1414-CT-0.0962-C-0.6163-O--0.5722-CT--0.0597-H-0.1997-H-0.1997-H-0.1997-HP-0.0889
Gaussian/AMBER Utility in Tools Menu
-HC-0.0300…
…
# Amber Opt

Atom Type and Partial Charge*** GaussianAMBER ***-2
1
N1-6.778000
C2-6.878000
C3-5.557000
O4-4.640000
C5-7.165000
H6-5.778000
H7-7.214000
H8-7.273000
H9-7.677000
H10-7.347000…
…

# Amber Opt-1.424000-0.708000-0.840000-1.504000
0.737000-1.527000-2.365000-0.879000-1.140000
1.267000

4.200000
2.896000
2.138000
2.579000
3.141000
4.462000
4.112000
4.933000
2.309000
2.189000*** GaussianAMBER ***-2

Delete serial
number

1

N
C
C
O
C
H
H
H
H
H
…
…

# Amber Opt-1.424000-0.708000-0.840000-1.504000
0.737000-1.527000-2.365000-0.879000-1.140000
1.267000

4.200000
2.896000
2.138000
2.579000
3.141000
4.462000
4.112000
4.933000
2.309000
2.189000

Paste atom type
and partial charge*** GaussianAMBER ***1
N-N3-0.1414
C-CT-0.0962
C-C-0.6163
O-O--0.5722
C-CT--0.0597
H-H-0.1997
H-H-0.1997
H-H-0.1997
H-HP-0.0889
H-HC-0.0300…
…

-6.778000-6.878000-5.557000-4.640000-7.165000-5.778000-7.214000-7.273000-7.677000-7.347000-2-6.778000-6.878000-5.557000-4.640000-7.165000-5.778000-7.214000-7.273000-7.677000-7.347000-1.424000-0.708000-0.840000-1.504000
0.737000-1.527000-2.365000-0.879000-1.140000
1.267000

4.200000
2.896000
2.138000
2.579000
3.141000
4.462000
4.112000
4.933000
2.309000
2.189000

Gaussian/AMBER
calculation

----- Ver.18.5.2 --------- Ver.18.5.1 -----

February 1, 2014 Minor bug fixes version
December 14, 2013

Fragments which have lower interaction energies than specified threshold can be displayed as
white translucent models. The translucency can be adjusted by alpha value (default=0.1).

P=0
M=0

P=1
M=0

P=1
M=-1

----- Ver.18.4.1 -----

October 19, 2013

(1) Residue name and number in PDB can be utilized for FMO fragment name. This function isuseful especially when residue number starts from other than 1.
FMO Menu > PDB Utilities >Residue Sequence Viewer

Residue name, number and theatom number of alpha carbon are
saved as RSQ file.

Load RSQ file, before making
FMO fragment.
RSQ file(2) FMO Fragment can be colored according to the interaction energies. To enable this function,
see FMO 2D Map of Fragment Interaction panel.

----- Ver.18.3.1 -----

August 31, 2013 Bug fix----- Ver.18.2.1 -----

August 17, 2013

(1) Visualization of fragment properties and pair interaction energies in solution,
computed with FMO/PCM.
Monomer surface areas (in A**2), charges (a.u.) and solute-solvent energies (kcal/mol).
I
surf_cav disp/rep surf_es cover,% q_cav eps_eff
Ges
Gcav
Gdisp
Grep
Gsol
---------------------------------------------------------------------------------------------------------------------------------------------------------------------1 (GLY-1
)
55.0
105.7
39.1
7.9 -0.8320
5.953 -55.839
7.797-5.3930.887 -52.549
2 (TYR-2
)
139.9
107.5
56.6 11.4 -0.1865
0.000-7.014 18.871-7.1981.038
5.697
3 (ASP-3
)
78.5
56.3
36.3
7.3
0.63642.750 -44.025 10.512-3.1980.516 -36.195
4 (PRO-4
)
82.5
84.7
34.1
6.9 -0.1293
0.000-0.670 11.404-5.161
0.761
6.336
5 (GLU-5
)
107.6
159.1
74.4 15.0 1.0617 -16.207 -71.093
14.511-9.2631.424 -64.421
6 (THR-6
)
76.1
72.0
38.5
7.8
0.31860.000-7.465 10.432-4.0050.590-0.4487 (GLY-7
)
44.3
41.2
22.4
4.5
0.13170.000-4.3755.997-2.1660.369-0.1748 (THR-8
)
87.0
95.8
41.6
8.4
0.08770.000-6.946 11.989-5.6400.837
0.240
9 (TRP-9
)
161.9
206.9
85.6 17.3 -0.2301
0.000-6.334 21.831 -13.948
1.924
3.473
10 (GLY-10 )
95.2
124.5
66.9 13.5 1.0956 -10.459 -85.693
12.682-7.004
1.154 -78.860

Ref.

J. Phys. Chem. A 2012, 116, 704-719. D. G. Fedorov and K. Kitaura"Energy Decomposition Analysis in Solution Based on the Fragment Molecular Orbital Method"

----- Ver.18.1.1 -----

July 3, 2013

(1) Quaternion Rotation
Rotations of molecular model in 3D by mouse movement was completely revised andquaternion rotation has been implemented. With this revision, all the problems related to 3D
rotation has been fixed.
(2) Lissajous Motion

Utilities Menu

Having implemented quaternion rotation,very complex rotation, such as Lissajous
motion is now possible. This feature is usefulfor demonstration of molecular models.

3D Trajectory of Lissajous motion
simulated by Mathematica

Controller of 3D Lissajous Curve Parameters(3) Orthographic Projection
Orthographic projection was also completely
revised and mouse click operation, such as atom
selection, is now possible as in perspective
projection.
The background color of Facio's Worksheetchanges according to the projection type.

white

cream

Perspective

Orthographic

Preferences Menu

(4) Input Orientation and Standard Orientation
There are two coordinate systems in Gaussian, i.e. input orientation and standard orientation.
When you see structural change during geometry optimization process, input orientation issuitable. If you use standard orientation for this purpose, you will see sudden structuralchange. ( cf. NoSymm keyword will prevents such molecular reorientation. )On the other hand, when you see dipole moment, standard orientation is required. If you use
input orientation instead, incorrect vector will be displayed.

----- Ver.17.1.2 --------- Ver.17.1.1 -----

May 29, 2013 Bug fix
May 3, 2013 New GUI for FMO 4.3

For backward compatibility, GUI for FMO 4.1 or before is still available. See FMO menu bar.

----- Ver.16.4.2 --------- Ver.16.4.1 -----March 30, 2013 Bug fixes and some modifications
Aug 8, 2012 Bug fixes and some modifications

----- Ver.16.3.1 --------- Ver.16.2.1 --------- Ver.16.1.1 -----

Aug 4, 2012 Bug fixes and some modifications
May 26, 2012 Bug fixes and some modifications
March 30, 2012

(1) New function to find neighboring FMO fragments within specified distance and save them as PDB.

----- Ver.15.1.2 -----

January 22, 2012

Compatible with GAMESS VERSION = 11 AUG 2011 (R1)----- Ver.15.1.1 ----- July 18, 2011
(1) User defined substituent

Example to make1-adamantyl fromadamantane

Change atom #17 to #1 with
Utilities menu >> Reassign
Atom Numbers.

Save as User Defined
Substituent from File menu

How to use : Place check mark on User Defined Substituent of "Replace H with" in Edit menu.
Then click the hydrogen to be substituted. Substituent list will appear. Select substituent you want.
(2) RMS fit
Geometry Comparison >>Load Two Molecules for Geometry Comparisonin the Utilities menu

Geometry Comparison >> RMS Fit by Quaternion
in the Utilities menu

Different Colors for
Two Molecules in
the Models menu.

Drag & drop two structures to be compared.
(3) Compatible with new FMO 4.0 features (gradient and optimization with PCM, and empiricaldispersion correction )(4) Max and RMS gradient changes during optimization are shown as a graph, such as below.

EnergyEnergy seems to be converged...

Max Gradient

But it's not yet.

RMS Gradient----- Ver.14.3.3 -----March 28, 2011 Bug fixes and new representation of hydrogen bond.

Bond Properties in Preferences menu

Hydrogen bondHighlighted atom and its coordinate----- Ver.14.3.2 -----

November 6, 2010 Bug fixes and toroidal fullerene models

Toroidal Fullerenes

C200
C120

C588

C640

----- Ver.14.3.1 -----

July 1, 2010

(1) New feature of PDB Utilities
It can find contacting water within a specified distance from solvated molecule.
For example, solvated protein is divided into protein molecule only PDB and water molecules only
PDB. Using these two files, Facio will search and find contacting water within a specified distanceand save as a PDB file.

protein molecule only

Protein in asolvationbox of water.
A result of
AMBER MD
calculation.

Contacting water
within 3 Angstromsof protein surface

Protein and thecontacting water

water molecules only

Contacting waters can be used as EFP (Effective Fragment Potential) of Gamess/FMO calculation.
For such calculation, input file can be automatically created. Just specify the PDB file of thecontacting water by clicking "Load Water for EFP" button in the FMO control panel.
(2) FMO fragments shown in Local Structure Viewer and atoms found in Closely Located Atoms
panel can be saved as a PDB file.
Frag142-143

Frag1-4
Frag44-46

Four fragment groups are extracted
and saved as a PDB file.
Frag20-22

Atoms within 6 Angstroms of the atom #145
are extracted and saved as a PDB file.

----- Ver.14.2.4 --------- Ver.14.2.3 --------- Ver.14.2.2 --------- Ver.14.2.1 -----March 19, 2010
March 14, 2010
January 9, 2010
December 25, 2009

Bug fixes
Bug fixes and some modifications
Compatible with Firefly (PC GAMESS) 7.1.G(1) Any part of FMO's PIEDA 2D map can be extracted and shown in new window as shown below.

Save as graphics

Setting rangeof fragment

Check to show partially extracted 2D map(2) Two-body FMO properties can be saved as reloadable file for Facio in Gamess version = 24
MAR 2007 (R6) format. See FMO menu >> Save PIEDA in Gamess Output Format
This feature makes it possible to create FMO difference file from two FMO difference files.
To the name of output file, suffix '_PIEDA_' is added by default. If you want to use other suffix,
please edit SavePIEDA_Suffix parameter of [AppControl] section in the Facio.ini file.
(3) Molecular model editor function on Closely Located Atoms Viewer
This new feature makes it possible to edit partial molecular model created by Closely LocatedAtoms Viewer. How to use : select mode from Edit menu and type the relevant atom numberin the textbox, Atom1, Atom2, Atom3 and Atom4, then click Execute button.
Closely Located Atoms Viewer can find and show atoms which are within specified distancefrom specified atom.

----- Ver.14.1.1 -----

October 25, 2009(1) 2D map representation of two-body FMO properties has been fully revised :energy levels to determine colors of the map can be predefined by user. This newfeature makes it possible to visualize small energy difference as shown below.

New representation

Old representation

Checkbox to use predefined energy levels
which determine colors of the 2D map.
(Default = Checked)
If it is not checked, automatically definedenergy levels are used.

Editor to set energy level values.
Levels to be modified are relevant to the currently
displayed energies on the 2D map.
Symmetrize button is to symmetrize energy levels withrespect to positive or negative values.
All the energy levels are saved in the FMO2Dmap.ini in
the Facio's root folder.

----- Ver.13.1.2 -----

October 3, 2009 Bug fix version of 13.1.1

To Vista user (see ReadMe)

----- Ver.13.1.1 -----

September 24, 2009 Updated to be compatible with Gaussian 09 outputs----- Ver.12.2.1 ----- September 12, 2009
Algorithm of FMO fragmentation has been revised for very special cases, such as solid surface.
----- Ver.12.1.3 ----- August 22, 2009
(1) New feature of PDB utilities
To add hydrogen atoms in ATOM record format to nucleic acid PDB.
To convert bad name field of ATOM record of nucleic acid to proper one.
(2) The default behavior of hydrogen bond detection
It is determined by SkipHBondDetection parameter of [AppControl] section in the Facio.ini.
SkipHBondDetection=1 (Skip hydrogen bond detection)
SkipHBondDetection=0 (Execute hydrogen bond detection for every new structure)(3) New amino residues are available for Polypeptide Builder
Orn (Ornithine), Aib (Methylananine), Pca (Pyroglutamic Acid)
Hid (Histidine with hydrogen on the delta nitrogen)Hie (Histidine with hydrogen on the epsilon nitrogen)cf. His (Positively charged Histidine with hydrogens on both the nitrogens)(4) Facio on Macintosh
It was confirmed that Facio can work on Intel Mac with a help of Darwine, which allows Mac
OS X to execute Windows native softwares. See the screenshot below.

Darwinehttp://www.kronenberg.org/darwine/

Please notice that Darwine requires X11, the X window system. But it is usually not installedby default. So, please make sure to install X11 from your Mac OS X install CD.

On Darwine environment, two problems are known up to now.
(a) Slide boxes in the main window are invisible.
But the slide boxes can work well. So, there is practically no problem.
(b) Drag & drop operation does not work.
This may be a problem of Darwine.
(5) Batch job control feature for Gaussian on remote server has been completely revised. In the
new version, user has to specify batch job script file by setting parameter BatchJobScript in
Facio.ini. Script file name should be relative to the Facio root folder. For example, if you
want to use xxx.jcf in JCF folder at Facio root folder, please set the parameter as follows.
BatchJobScript=JCF¥xxx.jcf

----- Ver.12.1.2 -----

July 13, 2009

Bug fix version of 12.1.1----- Ver.12.1.1 ----- June 27, 2009(1) Pull-down menu items have been fully revised and organized properly into submenus.
(2) For Tinker 5 user, set Tinker5 parameter of [AppControl] section in the Facio.ini file to 1. For
Tinker 4.2 user, set the parameter to 0. Default setting : Tinker5=1(3) A new coarse-grained model ( Trapezoidal Quad representation ) of protein
Each amino residue consists of four points (C and O of amide carbonyl, alpha C, and N ofamide), which is called as Trapezoidal Quad. Type of amino acid is represented by color.
Although you can use different color for different amino residue, use of four or five colors (forexample, hydrophobic, aromatic, basic, and acidic) are recommended.
For TQ representation, no missing hydrogen atom should be present. If there are missinghydrogen atoms, please complete them.
1BL8.pdb

Ball & Stick model

Trapezoidal Quad model(4) New function to find closely located atoms around a specified atom and to show them.

This example shows closely located atoms
within a radius of 4 Angstroms around apotassium atom of 1BL8.pdb(5) Visualization of MOs calculated with MOPAC2009/PM6, which has parameters for 70
elements( from H to Ba, La and Lu, and from Hf to Bi).
Transition metal complex models constructed from scratch only with Facio and
MOPAC/PM6 are included in the folder named "MetalComplexes_by_PM6".

----- Ver.11.8.8 -----March 27, 2009----- Ver.11.8.7 -----March 25, 2009

Bug fix version of 11.8.7(1) Facio now supports AFO (Adaptive Frozen Orbital) method, which is a newly developed FMO
fragmentation scheme and implemented in Gamess from version of Jan. 12, 2009.
Reference for AFO
Dmitri G. Fedorov, Jan H. Jensen, Ramesh C. Deka, and Kazuo Kitaura
J. Phys. Chem. A 2008, 112, 11808-11816(2) Up to Facio 11.8.6, atom colors and diameters of H, C, N, O, F, P, S, Si, Br, I were defined in
Facio.ini. From 11.8.7, all the atom colors and diameters of Ball-and-Stick type molecularmodel are defined in AtomProp.ini. If you want to customize these atom properties, please
use All_Elements_Colors.pdb, which is a virtual molecule as shown below and included in
Facio's distributing archive as sample molecule.

H
I

Si

X (Unknown Atom)PODu (Dummy Atom)

N
Li

Be
Br

S

C

F

He

B

Ne

Cl
Sc

Ti

La

Lu

(3) For naming of FMO fragments, the information of residue name and number in protein PDB
can be preserved in newly defined RSQ (residue sequence) file. See also Miscellaneous Menu>> Highlight PDB Residue Sequence for creation of RSQ file.
(4) Zoom in and out can be automatically performed according to the size of a molecule loaded.
(5) New function for FMO : You can load two Gamess/FMO outputs and create difference file offragment-fragment interactions.
(6) When effective core potential type basis functions, such as SBKJC and HW are used,sequential number of MO is different from the one based on usual type of basis functions.
Now Facio can respond to this change and show correct sequential number of MO.
(7) You can load Gamess input file to retrieve the structure in Cartesian coordinate.

----- Ver.11.8.6 -----

December 13, 2008

(1) A new chemical file format, FCC ( Facio Cartesian Coordinate ) has been created in order tostore Cartesian coordinates of GAMESS or Gaussian calculation without any truncation of thevalues and complete connectivity of the compound.
The following example of FCC is created based on a H2O calculated with Gaussian.
Facio Cartesian Coordinate :3O
10.0000000000
H20.7540650000
H3-0.7540650000

C:\G03W\Facio\H2O.out
0.1146870000-0.4587490000-0.4587490000

0.0000000000
0.0000000000
0.0000000000

2
1
1

3

The 1st line should contain string “Facio Cartesian Coordinate”. You can write a comment after
the colon of the 1st line. The 2nd line contains the number of atoms. After the 3rd line, eachcontains a kind of the atom, serial number, Cartesian coordinates and connectivity in thefollowing format.
A3, I7, 3(F17.10), n(I7)( where n is the number of bonds and varies from 0 to 8 )Cartesian coordinates can be saved as a number which has 10 digits after the decimal point. Thisfeature is useful for recording Cartesian coordinates of GAMESS or Gaussian outputs. The
connectivity data is also useful for complete reconstruction of the structure. Thus, FCC ( Facio
Cartesian Coordinate ) is suitable chemical file format of computational chemistry.
(2) Definition of FMO fractioning points (BDA and BAA) is now performed by clicking bondwhich you want fraction. Which of the two atoms is set to be BDA (Bond Detached Atom) is
determined automatically.
(3) FMO input file is now concurrently loaded to retrieve Cartesian coordinates of the compound
during loading FMO output which contains no geometrical data. Since all the information
about FMO fragment, such as INDAT(1), FRAGNAM(1), $FMOBND (if any), are also
obtained, you can see whole the fragments with Local Structure Viewer without
re-fragmentation with Facio.
(4) New ini keys, AddPause2Bat and UseFacioDriveLetter are introduced to [AppControl] sectionof Facio.ini.
AddPause2Bat determines whether add or not “pause” commant to the batch file which
invoke Tinker-MM3 calculation. If you want to insert pause after MM3 calculation finished,please set AddPause2Bat=1 (default value is 0).
UseFacioDriveLetter determines whether use of not the drive letter of Facio as the drive letter
for GamessBase or TinkerBase. For example, When GamessBase=C:¥PCGAMESS, the drive
letter of PC GAMESS is C:.But if you set UseFacioDriveLetter=1, the drive letter varies
according to the drive letter where Facio resides. Thus if Facio is installed at F: drive,
GamessBase is set to be F:¥PCGAMESS, even if it C:¥PCGAMESS in Facio.ini.
This feature is especially useful, when drive letter can vary due to the login environment.
(5) A new “Monitor Energy Conv.” button in the Gamess Input Option panel is cerated. With thisbutton, you can monitor energy/geometry change during the optimization process.
(6) When Tinker-Amber, Charm, Oplsaal input file is created, the batch file to invoke thecalculation and key file is now also created.

----- Ver.11.8.5 -----

November 8, 2008

(1) While the number of grid point per 1 angstrom to draw MO lobe using coefficients of MO was
fixed to 10 up to Ver. 11.8.4, now the value is customizable. In addition to this change, default
values of the two parameters in $VEC/Molecular Orbital Viewer (surface thickness andisosurface value) was revised.
(2) FMO fractioning points can be specified with clicking bond which has two atoms to be set to.
Which atom is to be BDA (Bond Detached Atom) is determined automatically by judging thekind and configuration of the atoms.
(3) 3D rotation via mouse move was revised.
(4) Mouse drag with holding down ALT key can translate molecular model in the monitor plane.
Sensitivity to the mouse drag is controlled with the parameter TransSens in Facio.ini file.
(5) Periodic Table of the Elements was revised.
(6) The format of Normal Coordinate Analysis are completely different between MOPAC
Ver.7.101 and MOPAC Ver. 8.211, as shown below. Now Facio supports this new format.
(MOPAC Ver.7.101)
NORMAL COORDINATE ANALYSIS

Root No.

1

2

3

4

5

6

7

8

1 E2u

1 E2u

1 B1g

1 E2g

1 E2g

1 A2u

1 E1g

1 E1g

341.2

341.2

582.1

589.4

589.4

768.9

899.2

899.2

1 0.0000 0.0000 0.0000 -0.0039 0.0714
2 0.0000 0.0000 0.0000 -0.0804 0.0655
3 -0.0442 -0.0581 -0.0415 0.0000 0.0000
4 0.0000 0.0000 0.0000 -0.0159 0.0698
5 0.0000 0.0000 0.0000 -0.0593 -0.0855

0.0000 0.0000 0.0000
0.0000 0.0000 0.0000
0.0129 -0.0326 -0.0019
0.0000 0.0000 0.0000
0.0000 0.0000 0.0000(MOPAC Ver.8.211)
MASS-WEIGHTED COORDINATE ANALYSIS (NORMAL COORDINATES)

Root No.

1
2
3
4
5

1

2

3

4

5

6

7

8

1 E2u

1 E2u

1 E2g

1 E2g

1 B1g

1 A2u

1 B2u

1 E1g

367.0

367.0

591.5

591.5

598.7

800.0

916.0

922.6

0.0001-0.0003-0.21900.0002-0.0003-0.00030.00050.41210.0003-0.0005

0.31550.2970-0.00020.3091-0.3687

0.00790.3506-0.0004
0.06380.27420.0002-0.0004-0.3130-0.00020.00040.0001-0.0001-0.11360.0001-0.0001-0.1976-0.34230.0005-0.1977
0.34230.00010.0001-0.0315-0.0001
0.0001

----- Ver.11.8.4 -----

October 4, 2008

(1) You can drag-and-drop Gamess/FMO output on the main display of Facio to read the file.
(2) When you load Gaussian output of a calculation with key words, Opt Freq, the initial structure
was shown instead of the optimized structure. This bug has been fixed.
(3) Upper limit of the parameter MAXIT of WinGamess is 200. But the value 300 is shown in theoption panel. This has been fixed. Please note that MAXIT=300 is acceptable for PC GAMESS.
(4) When you make an input of QST2 or QST3 calculation of Gaussian, comment lines of Productand Initial_TS are same as Reactant. This has been fixed.
(5) When you open IRC Data Viewer, CPU usage become nearly 100%. And when IRC Data
Viewer is opened, in some case, atom cannot be selected by mouse click. These have been fixed.
The same bugs found at Trajectory Viewer have also been fixed.
(6) The EIGENVECTORS format of MOPAC Ver.7.101 and that of MOPAC Ver.8.211 arecompletely different, as shown below. Now Facio supports this new format.

(MOPAC Ver.7.101)
Root No.

S
Px
Py

C
C
C

7

8

9

10

11

12

13

14

1 b2u

1 b1u

2 e1u

2 e1u

1 a2u

2 e2g

2 e2g

1 e1g

-15.732 -15.068 -14.200 -14.195 -13.161 -11.940 -11.936-9.639

1 -0.2149 0.0001 -0.0704 -0.0023 0.0000 0.0112 -0.0005 0.0000
1 0.0000 -0.4079 0.0040 -0.1309 0.0000 0.0191 0.3594 0.0000
1 -0.2241 -0.0001 0.4662 0.0148 0.0000 0.3397 -0.0182 0.0000(MOPAC Ver.8.211)
Root No.

S
Px
Py
Pz

C
C
C
C

1
1
1
1

7

8

9

10

11

12

13

14

1 b2u

1 b1u

2 e1u

2 e1u

1 a2u

2 e2g

2 e2g

1 e1g

-15.730-15.067-14.197-14.196-13.160-11.941-11.933-9.638-0.21460.0000-0.2233
0.0008-0.00020.40900.00040.0009-0.0014-0.1275
0.0085-0.0002-0.07020.00190.4667-0.00150.0002-0.00130.00070.40830.00020.35950.00550.0014-0.01100.0059-0.34020.0004-0.0004
0.0011-0.0017-0.5319

----- Ver.11.8.2 and Ver.11.8.3 -----

August 19, 27, 2008

These are minor bug fix versions of Ver. 11.8.1 and Ver.11.8.2, respectively.
----- Ver.11.8.1 -----

July 25, 2008

(1) New function to show all the intermediate geometries sequentially with the corresponding
energies when GAMESS or Gaussian optimization output file is loaded. Even if the calculation
is not finished, the output can be loaded. If MP2 energy is available, MP2 energy is also
displayed.
The retrieved intermediate geometries are stored as Opt_1.pdb, Opt_2.pdb, Opt_3.pdb…in
Facio’s base folder¥PDB¥OptResults, which is automatically created.
(2) Geometric information lists (bond length, bond angle and dihedral angle) are generated forplural files. Loadable file formats are PDB, CC1, Free formatted / WebLab xyz, MDL mol,
Tripos mol2, TINKER XYZ, GAMESS output and Gaussian output.
To use the function, select Utilities Menu >> Load File(s) and Dump Geometric Informations(3) Point mutation of protein
Load PDB file of protein in ATOM record and change the side chain of the specified amino
residue to that of the new amino residue and save as PDB file in ATOM record. Atom numbers
are automatically renumbered. If there are CONECT record for S-S bond of Cys-Cys,
CONECT record are also revised accordingly. In case the new amino residue is Glu, Asp, His,
Lys or Arg, there is an option to decide whether protonation is performed or not. When theside chain of the new amino residue collide with the already existing chains, adjust “Rotation
angle about CA-CB bond”. (CA : alpha carbon, CB : beta carbon)
When one of the Cys of Cys-Cys is replaced, hydrogen atom is added to the remaining Cys andthe corresponding CONECT record is deleted. When Pro is substituted with other residue,hydrogen atom is added to the nitrogen. For N-term residue, two hydrogen atoms are added.
When the new residue is Pro, hydrogen on N is deleted and five-membered ring is prepared.
Please note that the formed ring structure is usually distorted. But you can modify the ring
structure by changing the rotation angle about CA-CB.
Suffix which shows point mutation
is automatically added to the output
file. For example, when Ser 4 ismutated to Asn, “_S4N” is added as
suffix, which is consist of old residue
and new residue in one-letter
notation.
Examples are included in the folder
Point_Mutation.

(4) 2D map representation of two-body FMO properties was revised.
(5) Up to 16 colors available for Rainbow Fragment representation(6) Automatic generation of input file for Tinker-OPLSAAL calculation.

----- Ver.11.7.1 -----

June 12, 2008

(1) 2D map representation of two-body FMO properties

Two-body FMO properties of non-PIEDA calculation can also be displayed.

(2) Rainbow Fragment representation
In this representation, each FMO
fragments are drawn using rainbow
colors (red, orange, yellow, green,cyan, blue and purple) which are
cyclically applied.
How to display Rainbow Fragment
1. Make FMO fragment.
2. Open Local Structure Viewer.
3. Define local structure “by FMO
Fragment”.
4. Check “Rainbow Fragment”.

(3) Automatic generation of input file for Tinker-Charmm calculation.
(4) When missing hydrogen atoms are completed in ATOM record, the already existing CONECT
records (if any) are preserved. The numbering in CONECT record is automaticallyrenumbered.

----- Ver.11.6.1 -----

May 10, 2008

(1) PDB Utilities (See FMO menu items.)(A) Utility to delete alternate locations in ATOM record of PDB
12
3
4123456789012345678901234567890123456789012345 (Columns)
ATOM
ATOM
ATOM
ATOM

18 CD1ATYR A 327
19 CD1BTYR A 327
20 CD2ATYR A 327
21 CD2BTYR A 327

16.886 14.518 -8.371
14.840 15.316 -5.413
15.466 14.119 -6.496
16.667 14.101 -6.351

Alternate Location Indicator
ATOM
ATOM

18 CD1ATYR A 327
20 CD2ATYR A 327

16.886 14.518 -8.371
15.466 14.119 -6.496(B) Utility to convert format of Atom Name Field in ATOM record of PDB
ATOM
ATOM
...
ATOM
ATOM
ATOM

ATOM
ATOM
...
ATOM
ATOM
ATOM

24
25

HB2 TYR A
HB3 TYR A

2
2-5.189-4.918-0.788 -1.616
0.937 -1.380

104 HG21 THR A
105 HG22 THR A
106 HG23 THR A

8
8
8

0.813
2.533
1.885

-5.501-5.563-4.21024 1HB TYR A
25 2HB TYR A

2
2-5.189-4.918-0.788 -1.616
0.937 -1.380

104 1HG2 THR A
105 2HG2 THR A
106 3HG2 THR A

8
8
8

0.813
2.533
1.885

-5.501-5.563-4.210-2.562-2.176-3.104-2.562-2.176-3.104(C) Utility to add hydrogen atoms in ATOM record format to protein PDB
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

1
2
3
4
5
6
7

N
CA
C
O
CB
CG
CD

PRO A
PRO A
PRO A
PRO A
PRO A
PRO A
PRO A

1
1
1
1
1
1
1

8.316
7.608
8.487
9.466
6.460
7.110
7.873

21.20620.72920.70721.45721.72323.00222.56921.53020.33619.09219.00520.211
20.66121.889

ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM

1 N PRO A
2 CA PRO A
3 C PRO A
4 O PRO A
5 CB PRO A
6 CG PRO A
7 CD PRO A
8 1H PRO A
9 2H PRO A
10 HA PRO A
11 1HB PRO A
12 2HB PRO A
13 1HG PRO A
14 2HG PRO A
15 1HD PRO A
16 2HD PRO A

1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1

8.316 21.206 21.530
7.608 20.729 20.336
8.487 20.707 19.092
9.466 21.457 19.005
6.460 21.723 20.211
7.110 23.002 20.661
7.873 22.569 21.889
9.407 21.194 21.355
8.144 20.515 22.375
7.255 19.678 20.535
5.606 21.397 20.832
6.082 21.739 19.173
6.341 23.772 20.853
7.744 23.411 19.853
7.219 22.614 22.778
8.698 23.275 22.092(2) FMO fragmentation is now possible for the systems, where there is no fractioning point, suchas a cluster of water or there are isolated atoms, like noble gas system.

----- Ver.11.5.1 -----

April 13, 2008

(1) Upgrade of visualization panel for FMO PIEDA

Fragment NameThreshold to set visibility of fragment names

All the PIEDA charts can besequentially saved as graphics.

Slidebox for setting threshold

Stacked Column Chart

In Tall Mode, the height of the panel is about
two times as long as in default mode.

Columns in the chart can be represented using bitmap patterns as shown below.
The bitmap files are included in the folder, Brush_BMP.
BM-1.bmp
BM-2.bmp
BM-3.bmp
BM-4.bmp
BM-5.bmp

Total Pair Interaction
Electrostatic Term
Exchange Repulsion
Charge-Transfer plus Higher Order Mixed Term
Dispersion Contribution

These are just 8 x 8 bitmap files. So, you can freely change thesebitmap patterns with other patters you like.

(2) FMO fragmentation of (A)-B-(C)-D, where (A) and (C) are BDA (Bond Detached Atom) is
now possible. Use “Expert Mode”, in the FMO Fragmentation Panel.
(3) Header file for OpenGL has been changed for compatibility with Windows Vista.
(4) CIF file is now loadable.
(5) The way to display a series of structure obtained by IRC with Gaussian was modified.
(6) GUI for setting folder for screenshot capture was changed.
(7) Outline font for showing numeric labels and atomic symbols(8) The behavior when TER record PDB is saved as HETATM/CONECT format was modified.

----- Ver.11.4.1 -----March 15, 2008

(1) Visualization panel for FMO PIEDA (Pair Interaction Energy Decomposition Analysis)

Cursor Box
Bar graph representing the interaction energy between a specified
fragment and all the other fragments.

Structure in the Facio’s main panel and fragment number in the Local
Structure Definer are changed synchronizing with the change offragment in this panel.
Pair Interaction Energy
Exchange Repulsion
Electrostatic
Charge Transfer AmountCharge Transfer

Dispersion

Values are interaction energy witha fragment in cursor box.

Half transparent representation
To make the unselected part transparent(2) Please notice that input file generated by Facio 11.3.1 for PIEDA calculation has an error.
(3) Automatic generation of input file for Tinker-Amber calculation.
For detail, see the samples and ReadMe.txt in the Tinker-Amber folder.

----- Ver.11.3.1 -----

February 10, 2008

(1) Completely revised algorithm of FMO fragmentation
Up to Ver. 11.2.1, when peptide consists of more than two strands, numbering of the fragment is
as shown in the scheme, where numbering is not sequential within a single strand.

1

2

4

3

5

The new algorithm can generate FMO fragments with sequential numbering as follows.

1

2

3

4

5

(2) New FMO input option panel
Fragmentation of saccharide

PCM calculation options

Options for parallel execution
FMO layer is assigned in the Local Structure Viewer control panel.
(3) Facio on Macintosh
It was confirmed that Facio can workon Intel Mac, which uses Intel x86
processors.
The recommended virtual machine to run
Facio is VMWare Fusion. See thescreenshot.
Besides VMWare Fusion, you can use
CrossOver
Mac
6.21.
On
this
environment, there are some problems.
(Menu bar and slide boxes in the main
window are invisible. ) But thepull-down menu is visible and slide boxes
can work well. Thus, they are practicallyno problem.

Options for high-layer

----- Ver.11.2.1 -----

November 3, 2007

(1) Optimization of FMO fragment
FMO fragment is optimized with semi-empirical MO (PM3) or ab initio MO (STO-3G, 3-21G,
6-31GG). Keeping the position of fractioning atoms, coordinates of hydrogen atoms are optimized.
Optimization of non-hydrogen atom is also possible. Dangling atoms in the fragment are cappedwith hydrogen or appropriate groups. (See below) Optimizations of a range of fragments or all
the fragments are performed successively.

Capped with H

FMO fragment, in which fuchsia
bonds are fractioning bond.

Cappedwith group

Carbonyl and alpha carbon are
capped with CH3 and CONH2,
respectively.
Radio buttons to determine
which fragment to be minimized.
Use local structure viewer 1 toset fragment number or a rangeof fragment.
(2) Hybrid orbitals for sp3 S
They are requisite when fractioning atoms contain sulfur. But in the previous version of Facio,
they are missing. Hybrid orbitals of STO-3G and MINI were kindly provided by Prof. Kitaura(Graduate School of Pharmaceutical Sciences, Kyoto University). Hybrid orbitals of 3-21G, 6-31G
and 6-31G(d) were built by the author of Facio. The former orbitals are obtained from Gaussian
NLMO of H2S2 and the latter ones are from GAMESS Edmiston-Ruedenberg LMO of H2S.
(3) FMO fragment definition file
When you manually set fractioning points for FMO calculation, or when you change fragment
charge which is sometimes wrong value and necessary to be fixed, or when you modify fragment
name which is automatically set, you would like to save those changes in a text file. This is a FMO
fragment definition file. If you load the definition file, you don’t have to set fractioning point,
fragment charge and fragment name any more. It is especially useful in the case that manual
definition of fractioning point is necessary.

----- Ver.11.1.1 -----

October 2, 2007

(1) GUI for FMO (Gamess)
Bond fractioning for polypeptide andpolynucleotide is automatically
performed.
For non-peptide and non-nucleotide,
you can manually define andundefine fractioning point for FMO
fragment.
Input file of FMO calculation is
automatically generated. For
each fragment, charge isestimated and name of fragment
is created based on the aminoacid residue(s) therein.
INDAT array which contains theinformation of atom member ineach fragment is set without any
consideration.

(2) Local Structure Viewer
Local structure is specified by a range of atom numbers or FMO fragment numbers. There are
four independent windows for the viewers. With this local structure viewer, you can edit large andcomplex molecules, such as protein, much easily.

1fkb.pdb (Rapamycin - FKBP12 complex)
In the above screenshot, FMO fragment #55, #19, #4 and #22 are shown in each viewer. In thewhole molecule in the main window, the corresponding local structures are displayed in Red,
Lime, Yellow and Fuchsia, respectively.

----- Ver.10.9.9 -----

July 22, 2007

(1) Utility for specification of SIMOMM layers in WinGamess/Tinker(MM3) SIMOMM andautomatic generation of input file for the calculation.

Select"SIMOMM
Layers"inCalculation menu to open the control
panel. To assign SIMOMM layers,
select layer in the panel and click atomin the main window. Atoms assigned toHigh Layer are shown in a red box.
Atoms which are not in a red box are
assigned to Low Layer. (In the example,
six carbon atoms of the aromatic ringare set to High Layer.) To define
SIMOMM layer, click Apply button.
To
executeWinGamess/Tinker(MM3)SIMOMM calculation, select "WinGamess" in
Calculation menu, make a checkmark on
SIMOMM and execute. Input file which
requires $TINXYZ and $LINK data is
automatically generated.
To load the structure of QM/MM whole
molecule, use "Load New WinGamess Output
for Bulk Model in SIMOMM Calc. " in the Filemenu. To load QM part only, load Gamess
output as usually.
(2) New version of batch utilities for drag-and-drop execution of GAMESS are released.
PCG_DDE.bat
WG_DDE.bat( for PC GAMESS )( for WinGamess )To execute GAMESS calculation, drag-and-drop input file(s) on it.
It accepts up to 9 GAMESS inputs and sequentially executes them.
(3) If you click multi display (see Facio 10.9.7) or multi MO display (see Facio 10.7.1), molecularmodel or MO lobe in the multi display is now shown in the main window.
(4) For animation representation of normal mode vibration, movement of atoms is modified so
as to be symmetrical to the equilibrium position. According to this change, the parameter"Frames per half cycle" is restricted to odd number.
(5) Default values of BondCriterion and HX_Max are changed to 2.1 and 1.5, respectively.
These parameters determine the existence of bond between atom X and atom Y. In case thatboth X and Y are non-hydrogens, BondCriterion is used. HX_Max is the parameter wheneither X or Y is hydrogen.

----- Ver.10.9.8 -----

July 6, 2007

(1) Energy changes during optimization are shown as a graph, such as below.
With this tool, you can recognize how geometry optimization proceeds and find abnormal
behavihor in SCF calculation, which causes difficulty of convergence.
Select "Summarize Energy Changes During Optimization" in Miscellaneous menu. This menu
item is enabled whenever output file of GAMESS or Gaussian are loaded.
Y-amplitude slide bar set the magnifying factor of the graph.

Click energy value in the box located at the right side, a red vertical line appears.
This vertical line indicate where the energy corresponds to the point in the graph. If you drag amouse in the energy value list, the red vertical line moves accordingly.

(2) Output file of Gaussian 90 and 94, which is different from Gaussian 98 and 03 can be read atleast for optimized geometry. Reading of other type data are not garanteed, since the author of
Facio does not have any output files or checkpoint files of Gaussian 90 and 94 to test.

(3) New version of Drag-and-drop execution utility for PC GAMESS (Multi_DDEG3.bat) arereleased. To start PC GAMESS calculation, drag-and-drop input file(s) on it.
It accepts up to 9 PC GAMESS inputs and sequentially executes them.

After Facio 10.9.9,
PCG_DDE.bat (for PC GAMESS)andWG_DDE.bat (for WinGamess).

Multi_DDEG3.bat

Drag
&
Drop

----- Ver.10.9.7 -----

June 16, 2007

(1) Multi display as show in the screen shot below has been implemented.
Select "Load New Multi File" in the File menu. "Load New Multi File" panel will appear.

To the list box of this panel, you can drag-and-drop up to 10 PDB, CC1, free formatted or
WebLab XYZ, MDL mol, Tripos mol2, TINKER XYZ, GAMESS output and Gaussian output
and mixture of them. If you lick "Load All" button, then listed molecules will be shown in themulti display. The movement of the molecule in each sub window is synchronized with that of
the main window.
Sizes and positions of multi display are automatically saved in MultiDisp.ini file at Facio's root
folder, when you close the Load New Multi File panel with Close button.
If there are display problems, please try to set graphics hardware acceleration back.
It will fix the problem.

(2) Slight modification of the GUI in GAMESS Input Option panel(a) "Clear button" for IFREEZ input field(b) SOLVNT parameter of PCM calculation(c) Text box for setting base file name of the calculation to be executed.

(3) Graphics format for saving scree shot are now PNG and Bitmap. In the previous version, thesewere JPEG and Bitmap. You can set the default value with isPNG parameter in Facio.ini.
asPNG=1 (default format is PNG)
asPNG=0 (default format is Bitmap)(4) Initial magmification is set by the parameter EyeZdiff in Facio.ini.
EyeZdiff=0 (default, maximum zoom-in level) (0 <= EyeZdiff <= 400)

----- Ver.10.9.6 -----

May 12, 2007

(1) Detection and visualization of hydrogen bonds are implemented.
Criteria for detection are as follows.
X --- H .... A(a)(b)( Atom X = N, O, F, Cl, Br, I and atom A = N, O, F, Cl, Br, I, S )HX_Max < Length ( X .... A ) <= H_BondCriterion
H_BondAngleCriterion < Angle ( X --- H .... A ）<= 180 degrees
Default values :HX_Max = 1.3 Angstroms H_BondCriterion = 2.5 Angstroms
H_BondAngleCriterion = 90 degrees

Detection of hydrogen bonds is automatically performed whenever new molecular structure
loaded. If you check "Show Hydrogen Bonds" in the Miscellaneous Menu, hydrogen bonds
are displayed as lines. See the screen shot below.

"Dump Hydrogen Bonds" in the Utilities Menu will output hydrogen bonding data (sequential
number, hydrogen bond length, and so on) as text file.

(2) Using Bondi's van der Waals radii and the equations below, van der Waals volume can be
caclulated.

V  V
vdw All Atoms A
VA 

4 3
1 2
R 
hi (3R  hi )3i  Bonded Atom 3

wherehi  R 

R 2  d i2  Ri2
2d i(3) XYZ format of WebLab ViewerLite is now a supported molecular structure file.

----- Ver.10.9.5 -----

April 27, 2007

(1) Simulated IR, Raman and VCD spectra can be saved as text file in three resolutions :COARSE ( 5cm**-1), MEDIUM ( 1cm**-1) and FINE ( 0.1cm**-1).
COARSE is the resolution of Facio's spectrum window.
(2) Additional parameter for TINKER/MM3 are newly produced in order to make molecularmechanics calculation of esters, carbonates and carboxylic acids possible. These parameters
are not optimized but will be useful for modeling of medium-sized lactone or polycarbonates.
Please append the contents of "Additional_MM3PRM.txt" to mm3.prm.
(3) Up to the previous version, MOPAC versions of FORCE calculation which Facio can read
were MOPAC2000, MOPAC93, MOPAC6, WinMOPAC3.0, 3,5 and 3.9. Each version of
MOPAC has a different output format of FORCE calculation. Now Facio supports
MOPAC2007, which has another different format.
(4) Facio visualizes molecular orbitals of MOPAC2007. Since Facio can generate graphics data
without using PSI-88, input key word, GRAPH is not required for MO visualization.
After geometry optimization, Facio can automatically load molecular orbital coefficients from
output file. So, you can visualize HOMO only with two mouse-clicks!
1. evoke MO viewer ----- 2. show MO
For loading MO coefficients, the only supported version of MOPAC is MOPAC2007.

----- Ver.10.9.4 -----

April 12, 2007

(1) Solvent-excluded surface volume and area calculated by MSMS are shown.
(2) If you utilize EM64T feature of CPU for PC GAMESS, set EM64T=1 in Facio.ini.

----- Ver.10.9.3 -----

April 7, 2007

(1) PC GAMESS input options which are useful for MRMP2 calculation are automatically set.
(2) PC GAMESS input option which enables EM64T feature of CPU is automatically set.
(3) Bug related to energy levels representation of ROHF calculation has been fixed.

----- Ver.10.9.2 -----

April 1, 2007

(1) Energy levels of alpha and beta MO in UHF
calculation can be separately displayed.
(2)

TDDFT calculation is possible in
WinGamess , VERSION = 7 SEP 2006
(R4). GUI for this is implemented.

(3) Original folder icons are included.

----- Ver.10.9.1 -----March 14, 2007

(1) GUI for relaxed PES Scan (Potential Energy Surface Scan) calculation of PC GAMESS is
newly implemented. It can permit you to set parameters for two dimentional scan. To visualize
energy profile of PES and the corresponding structures, use Tool Menu >> PES Scan Data
Viewer.

GUI is not available for WinGamess, since it is not able to perform PES Scan along internal
coordinate of bond angle and dihedral angle.

(2) Models of gas hydrate skeleton are included as sample. They were modeled with Facio fromscratch. Corresponding imaginary polyhedranes, which are intermediate of the models, arealso included.

Type I----- Ver.10.8.1 -----

Type H

Type II
February 4, 2007

(1) New feature of loading more than one Gaussian cube MO is implemented.
Select "Load Gaussian Cubes for MOs (in Multi File Drag-and-Drop Mode) to open
list box window. To this window, drag-and-drop Gaussian cube MO(s). Then click "Load All"button. Then use CUBE/Molecular Orbital Viewer in Tools Menu. This is very convenientfeature when you want to view only selected MOs.

Drag & drop Gaussian cube MO
files to the window.

(2) New feature of generating sequential Gaussian cube MOs is implemented.
See Gaussian Utilities in Tools menu. Load formatted checkpoint, check "Generate Sequential
Cube MOs, and set the range of MO by specifying "From" and "To" parameters. Then click"Execute" button to generate cube MOs. Each cube data is saved as a separated file with MO
number attached automatically to the file name.
(CubeGen radio button is automatically checked, if formatted checkpoint is loaded before.)(3) Molecular geometry can now be retrieved from Gaussian formatted checkpoint file.

----- Ver.10.7.1 -----

January 17, 2007

(1) Up to 20 MOs can be viewed simultaneously. (See the screen shot below) The movement of themolecule in each sub window is synchronized with that of the main window. Each MO can also
be automatically saved as bitmap files. The position and size of sub windows are automaticallystored in MultiMO.ini at Facio's root folder.

(2) View point controller is implemented. See Utilities menu. This numerically changes the view
point of the molecule. You can also lock the view point.
(3) Up to ver. 10.6.2, double run of Facio has been intentionally prevented. But now multi run of
Facio is allowed. This is very useful for viewing many molecules at the same time.

----- Ver.10.6.2 -----

December 10, 2006

(1) Drag & drop execution utility for PC GAMESS (DDEG4.bat) is now released.
(2) Bug related to NMOFZC in $MCQDPT of GAMESS input option is fixed.
(3) SYMLOC=.TRUE. and MVOQ=6 are automatically set when LOCAL=BOYS or POP
and GROUP is other than C1.

----- Ver.10.6.1 -----

November 23, 2006

(1) Atom number reassigning utility
In order to use this utility, select "Assign Atom Numbers" in Utilities Menu.
Set the "Start From" parameter (default=1), then click atoms of which just you want tochange the number and finally click the "Assign Atom #" button. You don't have to click all
the atom. The numbers of the atoms which are not clicked are automatically reassigned.
(2) GUI for PC GAMESS can now make an input for MRMP2 calculation.
Input options are automatically included to speed up integral transformation & effective Fockmatrix construction steps, which dominates the overall cost of CI and MCSCF calculation.
(3) GUI for changing Arrow properties.
Arrow is used to represent normal mode vibration or dipole moment.
(4) Schematic representation of MO energy levels can now be saved as PostScript file.
(5) GUI for MOPAC.

----- Ver.10.5.1 -----

October 8, 2006

(1) Full revision of OpenGL-graphics rendering routines has dramatically lowered CPU usage.
(2) Drag & Drop operation is supported for loading structure files. Supported file types are PDB,
CC1, CC2, free-formatted XYZ, MDL Mol, Tripos Mol2, GAMESS output and Gaussian
output.
(3) MDL Molfile and Tripos Mol2 files can now be used as input files.
(4) FORCE calculation data of MOPAC93 and MOPAC2000 can be read to show normal mode
vibration as animation. MOPAC6, WinMOPAC3.0, 3.5 and 3.9 were already supported in
Facio 9.8.3.
(5) Dipole moment are shown as an arrow.

----- Ver.10.4.1 -----

August 21, 2006

(1) Arbitrary cross section of MO can be shown as contour plot with a help of GNUPLOT.
Contour plot shown below is a cross section of C60 's LUMO.
Samples are included in the folder "CubeMO_CrossSection".
To Linux user : Set write permission for the directory where GNUPLOT executable resides.

8

6

4

2

0

-2

-4

-6

-8
-8

-6

-4

-2

0

2

4

6

8

In order to superimpose wire model of the molecule to the contour
plot of the cross section, appropriate software, such as Illustrator isrequired.
(2) Gaussian input file for Multi-Step Job is supported.
(3) Custom route section for Gaussian can be set up to 30 items and shown as list.
(4) Under symmetry restricted condition, there was a bug in automatic setting of parameter
NMCC in $GUGA group and parameter NELS in $DET group. The bug has been fixed.
(5) Compression format of Facio's distributing archive has been changed to ZIP for Linux user's
convenience.

----- Ver.10.3.1 -----

May 27, 2006

(1) Schematic representation of MO energy levels is implemented for GAMESS.
(2) Atom sequence numbers are displayed near each atom as numeric labels.
Try “Miscellaneous Menu >> Show Numeric Labels”.
(3) Input file formation for TDDFT calculation of PC GAMESS 7.0 are supported.
(4) Input file for GAMESS calculation can be reviewed and edited before calculation.
The base file name for calculation can be modified before calculation as well.
(5) Perioric table is included.

Try “Miscellaneous Menu >> Show Periodic Table”.

(6) New atom colors for X atoms (other than H, C, N, O, F, Si, P, S, Cl, Br, I).
(7) Guide marker for molecular modelling.

Try “Miscellaneous Menu >> Show Guides”.

(8) Molecular models of Organometallics newly created with Facio are included as samples.

----- Ver.10.2.1 -----

Apr. 16, 2006

(1) Moment inertia of a molecule is calculate and the principal axes transformation is performed.
(2) Comparison of two molecule which are the identical molecule but have slightly different
geometry is performed and the geometrical differences (bond length, bond angles and dihedral
angles) can be saved as a text file.
(3) Schematic representation of energy level of molecular orbitals are modified.
(4) H-H coupling constants are extracted from Gaussian output file and saved as a texe file.
(5) Molecular structure can be extracted from “finished but not converged” or “not finished”
Gamess geometry optimization.

----- Ver.10.1.1 -----

Mar. 5, 2006

(1) Facio is now working on Linux (Fedora Core 4 and Scientific Linux 4.2)
with a help of WINE and Mesa.
WINE: http://www.winehq.com/
Mesa: http://www.mesa3d.org/

(2) A new GUI for UTChem. UTChem is a software package for ab initio quantum chemistrycalculation, developed at Hirao's Laboratory of Tokyo University.
http://utchem.qcl.t.u-tokyo.ac.jp/(3) PC GAMESS(Ver.7.0), MSMS and Tinker/MM3 on Linux can be executed from Facio on
Linux.
(4) Animated graphics of normal mode vibration can be sequentially stored as JPEG files.

----- Ver.9.9.1 -----

Dec. 25, 2005

(1) Molecular models of icosahedral higher fullerenes (C80, C180, C240, C320, C500, C540, C720,
C960, C980, C1280) are newly assembled from scratch with Facio.
(2) GIAO isotropic shielding values calculated with Gaussian / WinGamess are read in andchemical shifts relative to the TMS absolute shielding value are shown in table.

----- Ver.9.8.9 -----

Nov. 29, 2005

(1) It was found again that there are cases where vibrational vectors of Gaussian normal mode
calculation are not properly read. This bug has been fixed.

----- Ver.9.8.8 -----

Nov. 28, 2005

(1) Resolution with which intensity and wave number of IR, Raman and VCD are saved as text
file is changed from 5.0 (1/cm) in the previous version to 0.1 (1/cm).
(2) It was found that there are cases where vibrational vectors of Gaussian normal mode
calculation are not properly read. This bug has been fixed.

----- Ver.9.8.7 -----

Nov. 12, 2005

(1) The way to display a series of structure obtained by IRC calculation with Gaussian ismodified.
For example, if the calculation was performed for 13 points on IRC, results are stored in theformatted check file in the order of 7-6-5-4-3-2-1-8-9-10-11-12-13, in which the structure #7
corresponds to the transition state. The older version of Facio displays these structures in theorder as stored, i.e. 7-6-5-4-3-2-1-8-9-10-11-12-13. Ver.9.8.7 displays them in the order of
1-2-3-4-5-6-7-8-9-10-11-12-13 so as to show continuous change of the structures.
(2) In IRC display mode, inter atomic distance, bond angle and dihedral angle are incorrectly
measured. This bug has been fixed.
(3) Trajectory data obtained by ADMP or BOMD MD calculation with Gaussian can be visualized.
Energy changes (nuclear kinetic energy, electron kinetic energy, potential energy and totalenergy) are plotted along the time in trajectory.
(4) Cartesian coordinate 1 and 2, and "free formatted XYZ" file are newly supported as an input
file.
Free formatted XYZ file is a simple XYZ file, in which each line consists of only atom symboland x, y, z coordinates separated with at least one space. See the sample.xyz in the XYZ folder
in Facio folder.

----- Ver.9.8.6 -----

Oct. 2, 2005

(1) Intensity and wave number of IR, Raman and VCD can be saved as text file.
(2) You can see atomic number with “Miscellaneous Menu >> Highlight Specified Atom”----- Ver.9.8.5 -----

Sept. 24, 2005

(1) In a special case, CUBE MO data is incorrectly determined to be “truncated”
with the warning message “CUBE data may be truncated”, even if it is not so.
This bug has been fixed.

----- Ver.9.8.4 -----

Sept. 17, 2005

(1) GUI for Gaussian ONIOM Layer specification has been implemented.
(2) VCD(Vibrational Circular Dichromism) spectrum is simulated.
VCD calculations of d-Menthol and l-Menthol are included as example data.
(3) Displacement vectors of normal mode vibration are shown as arrows.
(4) You can use g03w.exe instead of g03.exe for command line execution of Gaussian.

----- Ver.9.8.3 -----

Aug. 27, 2005

(1) Completion of missing hydrogens has been implemented.
(2) Facio can read FORCE calculation data of MOPAC6,
WinMOPAC3.0, 3.5, and 3.9 to show normal mode vibration as animation.
(3) You can capture the screenshot of main window of Facio and save as JPEG file.
Unlike Windows' Alt-PrintScreen function, Facio's screenshot function excludes
window frame and menu bar.

----- Ver.9.8.2 -----

Jul. 9, 2005

(1) For transition structure search using the STQN method, the reactant, product,and initial TS structure can be specified through GUI.
(2) Facio has failed to read PDB file which has MODEL and CONECT records.
This bug has been fixed.

----- Ver.9.8.1 -----

Jun. 17, 2005

(1) SSH / SFTP client has been implemented. Through SSH / SFTP connection, Gaussian job can
be submitted to batch job system on the remote server and calculation results can be retrieved
form the server. Supported batch job systems are LoadLeveler and NQS.

----- Ver.9.7.6 -----

Apr. 18, 2005

(1) Facio and external programs can be installed in different disk drives each other.
For example, Facio in D: drive and PC Gamess in C: drive.

(2) User-customized position and size of main window and position of Facio’s worksheet
is saved in Facio.ini. See Edit menu >> Save Position and Size of Main Window(3) Edit Tool Box :Selected Edit Menu items are separated from menu and packed in a box which can beplaced anywhere in display. Edit Tool Box facilitates molecular modeling.
See Miscellaneous menu >> Show Edit Tool Box----- Ver.9.7.5 -----

Apr. 9, 2005

(1) Criteria to determine mesh representation of CUBE MO is now adjustable.
If no mesh representation is shown, please increase Mesh Criteria value.

----- Ver.9.7.4 -----

Mar. 12, 2005

(1) IRC data (in Gaussian formatted check file) is visualized.

----- Ver.9.7.3 -----

Feb. 26, 2005

(1) Electrostatic Potential CUBE data calculated with PC GAMESS or Gaussian 03W
is mapped onto Solvent Excluded Surface calculated with MSMS.
The following graphics shows this feature.

Electrostatic potential of Benzene mapped onto solvent excluded surface(2) With Facio Ver.9.6.1 and Ver9.7.1, PC GAMESS input file for CUBE electrostatic potential
andelectron density has not been calculated even if user properly sets input options.
This bug has been fixed.
(3) Utility which is useful for modeling of compound with symmetry are added.
With this utility, atoms which are within ApproxityCriteria are exactly
moved to Z axis. The parameter ApproxityCriteria is set in the Facio.ini.

----- Ver.9.7.2 -----

Feb. 5, 2005

(1) Visualization of Gaussian 03W CUBE molecular orbital and normal mode vibration
has been implemented. Graphical Viewer of MO level and multiplicity is also built in.
GUI for Gaussian 03W Utilities ( CubeGen, FormChk, FreqCheck ) are also created.
(2) Molekel is invoked within Facio.
(3) In the case that PC Gamess or WinGAMESS is placed in the folder whose absolute pathcontains "space", a required fonder (Facio) has not been properly produced. This bug
has been fixed.

----- Ver.9.7.1 -----

Jan. 22, 2005

(1) GUI for MCSCF calculation has been implemented.
Parameters in $DRT and $DET group are automatically set
according to the charge and spin multiplicity.
(2) GUI for Gaussian 03W has been implemented.
With this GUI you can make an input file (Gaussian job file, *.gjf) andstart the execution of the job.
Customized route section commands for individual user are stored in Facio.ini
as CustomRoute1, CustomRoute2, ... and CustomRoute9.
*** Visualization of Gaussian output, such as molecular orbitals andnormal mode of vibration will be implemented in the next version of Facio. ***(3) In the case of Gamess option $CONTRL NOSYM=0 and$DATA GROUP=(other than C1), Facio failed to readsome orbital energies. This bug has been fixed.
(4) Symmetry of molecular orbital is displayed in the MO Viewer panel.
(5) In the cases other than GROUP=C1, molecular orbital numbers of HOMO andLUMO have not been properly calculated. This bug has been fixed.
(6) Utility which is useful for modeling of compound with symmetry are added.
With this utility, atoms which are within ApproxityCriteria are exactly
moved to XY plane or YZ plane. The parameter ApproxityCriteria is
set in the Facio.ini.
(7) Winmostar is invoked within Facio.

http://winmostar.com/(8) Examples of compounds with symmetry are included in the SymmetryUniquefolder.
(9) In some cases, preferences has not been properly saved. This bug has been fixed.

----- Ver.9.6.2 -----

Nov. 14, 2004

(1) In the case of Gamess option $CONTRL NOSYM=0 RUNTYP=OPTIMIZE and$DATA GROUP=(other than C1), "COORDINATES OF SYMMETRY UNIQUE ATOMS"
are output. But the output format is slightly different between
PC GAMESS and WinGamess. And this diffecence causes an input error
when WinGamess output is loaded. This bug has been fixed.

(2) New checkbox is addedin the Menu>>Preferences>>External Programs.
When coordinates of symmetry unique atoms are available,
this checkbox determines whether only symmetry unique atoms are shown or not.
This option is valid only for "Load New Gamess Output".

----- Ver.9.6.1 -----

Nov. 7, 2004

(1) Interactive pre/post-processor for WinGamess has been implemented.
WinGamess is PC WIN32/GCC VERSION of GAMESS(VERSION = 19 MAY 2004 (R4))
precompiled under the Cygwin environment by Nuno A.G. Bandeira.
http://www.msg.ameslab.gov/GAMESS/dist.pc.html
Facio makes an input file and execute WinGamess job
with runscript.csh and ddikick.exe in the WinGamess package(2) When CUBE MO data is loaded from punch file, MO energies are alsoloaded from the corresponding output file.
There was no problem about this up to now. But it was found that
MO energies are not properly loaded in special cases,
for example,6-31G(d)/UHF calculation of ammonia cation radical. This bug has been fixed.

----- Ver.9.5.1 -----

Oct. 24, 2004

(1) Parameters in TINKER Key file is described as relative path name,when the absolute path name of TINKER parameter file contains "space",e.g. "C:\My Document\Tinker\params\amber.prm".
In such a case, the author assumes that the TINKER is
installed as follows.
Tinker ------ bin ------ optimize.exe|--- params --- mm3.prm|-- amber.prm(folder name 'bin' may be other name)orTinker ------ optimize.exe|--- params --- mm3.prm|-- amber.prm
In both case, folder name 'params' is fixed.
However, if the absolute path name of TINKER parameter file
DOES NOT contain "space", parameters in TINKER Key file is described
as absolute path name.

(2) Although alpha and beta orbitals are obtaied from UHF calculation,
only alpha orbitals have been taken in the preveous version of Facio.
Now Facio can display both orbitals of UHF calculation.
For ICORBS input data of GAMESS, Facio can automatically set
negative orbital numbers for beta orbital CUBE data and visualize them.
For example,
HOMO and LUMO of H2O radical cation is #5 and #6 MO, respectively.
If you set GAMESS input option of ICORBS in UHF calculatio as follows
HOMO-2 and LUMO+1,$ELDENS in the GAMESS input file will be$ELDENS IEDEN=1 ICORBS(1)=3, 4, 5, 6, 7,-3, -4, -5, -6, -7 $END
where negative numbers are corresponding beta orbitals.
About this new feature, I appreciate the useful suggestion ofProf. emeritus Ernst Schumacher (University of Bern), the author of
RUNpcg and Cygam which are the GUI for executing the GAMESS code.
http://www.chemsoft.ch/qc/RUNpcg.htm
http://www.msg.ameslab.gov/GAMESS/dist.pc.html(3) Zoom In/Out operation can be performed with mouse wheel.

----- Ver.9.0.1 -----

Sept. 12, 2004

(1) Interface to Tinker-MM3 calculation has been implemented.
So you can perform geometry opitimization with Tinker-MM3.
Atom types which Facio can recognize are ...
1 C
sp3 Alkane
2 C
sp2 Alkene
3 C
sp2 Carbonyl
4 C
sp Alkyne
5 H except on N, O, S
6 O C-O-H, C-O-C, O-O
7 O C=O Carbonyl
8 N
sp3
9 N
sp2 (Amide)
11 F Fluoride
12 Cl Chloride
13 Br Bromide
14 I Iodide
15 S -S- Sulfide
16 S+ >S+ Sulfonium
17 S >S=O Sulfoxide
18 S >SO2 Sulfone
19 Si Silane
21 H-OH Alcohol
22 C Cyclopropane
23 H NH Amine/Imine
25 P Phosphine

28
37
38
39
40
41
42
44
46
47
48
49
56
57
58
124

H
N
C

Amide
Pyridine
Cyclopropene(but bond stretching parameter 38-38 is undefined in MM3)
N+ N sp3 Ammonium
N N sp2 Pyrrole
O O sp2 Furan
S S sp2 Thiophene
H SH Thiol
N NitroO Carboxylate
H Ammonium
O Epoxy
C C sp3 Cyclobutane
C C sp2 Cyclobutene
C C=O Cyclobutanone
H C-H Acetylene----- Ver.8.7.1 -----

Jul. 30, 2004

(1) Mesh surface representation for MO, total electron density andelectrostatic potential has been implemented.

----- Ver.8.5.1 -----

Jul. 5, 2004

(1) Using RUNTYP=RAMAN option, you can calculate Raman intensities
with which Raman spectrum is simulated.
About this new feature, I appreciate the useful suggestion ofProf. emeritus Ernst Schumacher (University of Bern), the author of RUNpcg.
(2) In order to demonstrate the modeling ability of Facio,
highly complex molecular models for natural toxins listed below are
included in the folder PDB/Toxins. Not only the final structures but alsointermediate structures are included to show how I constructed them.
Brevetoxin-A
Maitotoxin
Okadaic Acid----- Ver.8.3.1 -----

Halichondrin-B
Neosurugatoxin
Pinnatoxin-A

Jun. 22, 2004

(1) Polynucleotide model is built from scratchwith a help of Tinker 3.9 (nucleic.exe).
Because of bugs in "nucleic.exe" module in Ver.4.1 and
4.2 (before minor revision: Sept. 8, 2004),
collision will occur between the complementarybase pairs for B-form double helix (base pairs >= 4)and Z-form one.
*************************************************For B-form double helix, the bugs have been fixedin the Ver. 4.2 (minor revision: Sept. 8, 2004)*************************************************

However, the bugs on Z-form have not yet been fixed.
(2) It was revealed that external programs cannot be run in the root folder.
Thus, Facio checks whether they are installed in the root folder or not
before enabling the menu item for them.

----- Ver.8.0.2 -----

May 31, 2004

(1) The scale of IR spectrum is shifted in some cases other thanJapanese Windows system and Lorentzian line shape of IR spectrum isincorrectly calculated. These bugs have been fixed.
About this bug fix, I appreciate the useful comment ofProf. emeritus Ernst Schumacher (University of Bern), the author of RUNpcg,
which is a graphical interface for executing the GAMESS code.
http://www.chemsoft.ch/qc/RUNpcg.htm
http://www.msg.ameslab.gov/GAMESS/dist.pc.html
RUNpcg is a 'Dialect' GUI to be used in conjunction with Gamess.
'Dialect' is a general purpose programming language that includes
an integrated development environment with debugging support.
http://www.downlinx.com/proghtml/104/10441.htm(2) Structure of an origosaccharide sample PDB (Raffinose.pdb)
was incorrect at the connection of fluctose and glucose.
Correct structure has been included in this version.

----- Ver.8.0.1 -----

Apr. 30, 2004

(1) Visualization of $CUBE/Molecular Orbitals which is the new feature of PC GAMESS 6.4.
(2) Bugs in deletion of isolated atom are fixed.
(2) Procedure AddHydrogen was modified.

----- Ver.7.5.1 -----

Apr. 5, 2004

(1) Glycosyl substituents are available for polysaccharide modeling.
(2) OH, Formyl, NH2 substituents are also available.
(3) Point group symmetry can be specified for GAMESS calculation.
Related parameters are GROUP and NAXIS. (GROUP=C1, CN only)(4) Array of Cartesian coordinates to freeze during
a geometry optimization will be set with a parameter IFREEZ.
(5) $STATPT METHOD=CONOPT with a parameter IFOLOWThis can be used for locating transition states.
(6) When GAMESS calculation terminated abnormally, the reason will be shown.

(7) $VEC data (MO coefficients) can be retrieved fromGAMESS punch file and pasted to input file with GUESS=MOREAD.
(8) When molecular geometry is adjusted, the current value is also shown.
(9) Auto Centering is OFF by default. For proteins or nucleic acids, default is ON.

----- Ver.7.0.1 -----

Mar. 11, 2004

(1) Polypeptide model is built from scratch with a help of TINKER's protein.exe
See the description of Tools Menu >> Polypeptide Builder.
(2) Interface to DFT calculation is implemented.
DFT calculation is a new feature of PC GAMESS ver.6.4.
(3) Molecular geometry can be adjusted more precisely.
For angle adjustment 0.1 degree is the minimum change andfor distance 0.001 angstrom, if "Fine adjustment" is checked.

----- Ver.6.5.1 -----

Feb. 9, 2004

(1) IR spectrum can be simulated with IR intensities data,
which is available in normal mode calculation.
How to use : see the description of Tools Menu >> Normal Mode Vib. Viewer.
(2) Total electron density can be calculated with semiempirical MOs.
GAMESS produces total electron density as CUBE data only when ab initio
calculation is performed. But this feature makes it difficult to visualize
the electron density of a very large molecule. Thus, the calculation ofelectron density using coefficients of semiempirical MO is implemented in
Facio 6.5.1.
How to use : see the description of Tools Menu >> Molecular Orbital Viewer.
(3) Bug fix in 'Delete Atom'.
Fatal exception sometimes occurred when solitary atom was deleted.
Solitary atom is an atom which has no bond to other atoms.

----- Ver.6.0.1 -----

Jan. 24, 2004

(1) $HESS group (Hessian Matrix) can be retrieved from GAMESS Punch
and attached to the GAMESS input file using GAMESS option HESS=READ.
(2) The number of Imaginary frequency is checked
after RUNTYP=HESSIAN calculation.
(3) IRC data (a series of structures obtained after RUNTYP=IRC calculation)is visualized.
(4) New GAMESS Input Options:$CONTRLRUNTYP=SADPOINT=IRC

$STATPTHESS METHOD$BASISNDFUNC NFFUNC NPFUNC DIFFSP DIFFS$IRCPACE SADDLE FORWRD NPOINT STRIDE(5) If optimized geometry or saddle point is available, coordinates will be
written in 15.10F format to the GAMESS input file for the next run.
If not, it will be written in 8.3F format as in PDB file.
Availability of the stationary point coordinates is shownin the GAMESS input option panel.
(6) You can select perspective projection or orthogonal projection.
Orthogonal projection is useful especially when you adjust
relative position and tilting angle of two separately loaded molecules.
See also Utilities Menu > "Adjust Position and Tilting Angle".

----- Ver.5.0.1 -----

Dec. 24, 2003

(1) Isovalue surface of electron density and electrostatic potentials
are displayed with dot surface representation.
(2) New GAMESS Input Options:
MESH

Specifies desired density of points
along each side of the cube.
Values are COARSE, MEDIUM, and FINE.

ELDENSELPOTElectron density is calculated.
Electrostatic potentials are calculated.

MORB

MORB=0(Generates Total Electron Density)
MORB=xxx (Generates Electron Density for MO # xxx)

(3) In the previous versions, Facio.ini was not read inon Windows XP. This bug was fixed.

----- Ver.4.7.1 -----

Dec. 11, 2003

(1) OpenGL rendering has been fully revised.
Result : For example, animation of normal mode vibration is displayedmuch faster than former versions.
Compare Ver.4.6.1 and Ver.4.7.1.
(2) On Germany or French system, Facio has been freezed.
This problem was fixed.
Some European countries use a comma for a floating point separator
instead of a period. In particular, StrToFloat function willcause an exception if the string passed to it has the wrong decimal
separator.
(3) Exception (e.g. access violation) occurred during the excution

of Facio is fully trapped. This feature can be customized byediting the following init record in Facio.ini.
[AppControl]
ExceptionMessage=ON
where
ON ===> Trap exception
OFF ===> Egnore exception(But Facio may be freezed in case of vital exception)(4) Visualization of electron density and electrostatic potential is
not yet implemented in Ver.4.7.1.

----- Ver.4.6.1 -----

Nov. 7, 2003

(1) Facio can be launched as a command line application, which
accepts one command line argument (i.e. pdb file) at run time.
How to use :MS-DOS prompt> Facio.exe xxx.pdb
where the xxx.pdb is a PDB file.
(2) Graphics rendering interval can be customized in Facio.ini file.
Since no GUI is provided for adjusting this parameter, please
edit the following init record in Facio.ini.
[Timer]Interval=50
This means that graphics are rendered every 50 microseconds.
If your graphics card does not have sufficient power,
try to set this parameter higher value, e.g. Interval=100.
If your graphics card have sufficient power,
you can set it lower value, e.g. Interval=30. In that case,Facio will more quickly respond to your mouse movement.
However, never set it 10 or lower : your machine may be freezed.
###### This feature is no more necessary for Ver.4.7.1 or higher ######(3) MODEL records in PDB file are recognized.
Only one model is displayed and other models are omitted for clarity.
(4) Hydrogen atoms of standard residues in PDB file areparsed to produce connectivity record.
(5) Hydrogen atom can be attached to lone atom.

----- Ver.4.5.1 -----

Oct. 17, 2003

(1) MO visualization is implemented for basis set MINI.
This means that MOs of all the atoms up to Rn can bevisualized. You can see 4f orbitals for lanthanides.

(2) New GAMESS input options(IREST and GUESS) are supported.
With input option IREST=-1, GAMESS execution can beeasily restarted where it left off.
(3) Several bugs about parsing Protein PDB files are fixed.