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Subject: RE: [NWCHEM] QM/MM geometry constraints
Date: Fri, 6 Jul 2007 15:29:36 -0700
Message-ID: <9EA84B4DE79CD74F89F814624913B70503AA1909@EMAIL01.pnl.gov>
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Thread-Topic: [NWCHEM] QM/MM geometry constraints
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From: "Valiev, Marat" <marat.valiev@pnl.gov>
To: "Mark Cunningham" <cunningham@utpa.edu>
Cc: <nwchem-users@emsl.pnl.gov>
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Dear Mark,

=20

Internally NWChem uses Cartesian geometry, as does QM/MM code.

The best way to constrain the distance between atoms is to use
constraint module

where one can put a spring between two atoms. The indexing is that of QM
geometry. The best way to get it is to run

single point energy and look either in the input file or *active.pdb
file.=20

=20

Here is an example. Let me know if it does not work.

=20

----------

=20

memory total 2000 Mb

start clfoh

permanent_dir  ./perm

scratch_dir /scratch

=20

charge -1

=20

basis "ao basis"

 * library "6-31+G*"

end

=20

dft

print low

XC b3lyp

iterations 5000

end

=20

task shell "cp clfoh_ps00.rst clfoh_rs00.rst"

md

 system clfoh_rs00

 cutoff 1.5 qmmm 1.5

 noshake solute

end

=20

constraints

fix atom 7

fix atom 6

fix atom 1

spring bond 1 5  3.0 1.89

end

=20

qmmm

region qm solvent

method bfgs sd

xyz    rs

maxiter 30 3000

density espfit

ncycles 20

end

=20

task qmmm dft optimize

=20

Marat Valiev, Ph.D.
Senior Research Scientist
Molecular Sciences Software Group (NWChem)
marat.valiev@pnl.gov
 =20

From: Mark Cunningham [mailto:cunningham@utpa.edu]=20
Sent: Friday, July 06, 2007 12:18 PM
To: Valiev, Marat
Subject: RE: [NWCHEM] QM/MM geometry constraints

=20

Dr. Valiev:

=20

I am interested in constraining the distance between two atoms in

the quantum partition.  Must I place an harmonic restraint on the=20

atoms? =20

=20

I thought that the QM/MM code invoked the standard

QM utilities to compute energies and the like and that NWChem

used internal coordinate representations internally.  Is there

some way to (manually) force an internal coordinate in the

QM part of a QM/MM calculation?  I could/would modify the

appropriate code if you can point me in the proper direction.

=20

Thanks for your help

=20

Mark Cunningham

=20

________________________________

From: Valiev, Marat [mailto:marat.valiev@pnl.gov]
Sent: Fri 7/6/2007 11:49 AM
To: Mark Cunningham; nwchem-users@emsl.pnl.gov
Subject: RE: [NWCHEM] QM/MM geometry constraints

Mark,

=20

QM/MM module does not use internal coordinates representation, thus your
errors.

Also aside the potential use, the actual charmm fragment files have
never been tested.

I would recommend using AMBER force field.

=20

Marat Valiev, Ph.D.
Senior Research Scientist
Molecular Sciences Software Group (NWChem)
marat.valiev@pnl.gov

 =20

From: owner-nwchem-users@emsl.pnl.gov
[mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of Mark Cunningham
Sent: Thursday, July 05, 2007 1:40 PM
To: nwchem-users@emsl.pnl.gov
Subject: [NWCHEM] QM/MM geometry constraints

=20

I am trying to use NWChem 5.0 to perform QM/MM calculations but my
progress

has been hampered by the fact that none of the examples in the
distribution

actually run.  Additionally, it appears that all of the CHARMM fragment
files are

incorrect.

=20

My problem at the moment is to specify a geometry constraint.  In an all
QM

calculation, I can use zcoord to force an atom-atom distance to be some
value

without having to use an harmonic restraint.  In a QM/MM calculation, I
tried using=20

the same strategy: after task prepare, I specified:

=20

geometry
   zcoord
      bond 77 153 3.5 constant
      torsion 69 71 77 153 178.12 constant
   end
end

This results in the following error:

User specification of redundant internal variables
 --------------------------------------------------

   i   j   k   l     value       name   frz
  --- --- --- --- ------------ -------- ---
   77 153             3.500000 User001    T
   69  71  77 153   178.120000 User002    T


 Scaling coordinates for geometry "geometry" by  1.889725989
 (inverse scale =3D  0.529177249)

  geom_cart_set: too many centers                      0 geometry
  geom_masses_set: too many centers                      0 geometry
  geom_nucexps_set: too many centers                      0 geometry
=20
------------------------------------------------------------------------
 geom_input: geom_nucexps_set failed        0
=20
------------------------------------------------------------------------
=20
------------------------------------------------------------------------
  current input line :
    42: end
=20
------------------------------------------------------------------------

I would appreciate any advice.

=20

Mark A Cunningham

The University of Texas-Pan American

=20


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<div class=3DSection1>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>Dear Mark,<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>Internally NWChem uses Cartesian geometry, as does QM/MM =
code.<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>The best way to constrain the distance between atoms is to =
use
constraint module<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>where one can put a spring between two atoms. The indexing =
is that
of QM geometry. The best way to get it is to run<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>single point energy and look either in the input file or
*active.pdb file. <o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>Here is an example. Let me know if it does not =
work.<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>----------<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>memory total 2000 Mb<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>start clfoh<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>permanent_dir&nbsp; ./perm<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>scratch_dir /scratch<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>charge -1<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>basis &quot;ao basis&quot;<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>&nbsp;* library &quot;6-31+G*&quot;<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>end<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>dft<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>print low<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>XC b3lyp<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>iterations 5000<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>end<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>task shell &quot;cp clfoh_ps00.rst =
clfoh_rs00.rst&quot;<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>md<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>&nbsp;system clfoh_rs00<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>&nbsp;cutoff 1.5 qmmm 1.5<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>&nbsp;noshake solute<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>end<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>constraints<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>fix atom 7<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>fix atom 6<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>fix atom 1<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>spring bond 1 5&nbsp; 3.0 1.89<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>end<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>qmmm<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>region qm solvent<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>method bfgs sd<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>xyz&nbsp;&nbsp;&nbsp; rs<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>maxiter 30 3000<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>density espfit<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>ncycles 20<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>end<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>task qmmm dft optimize<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:10.0pt;color:blue'>Marat =
Valiev,
Ph.D.<br>
Senior Research Scientist<br>
Molecular Sciences Software Group (NWChem)<br>
marat.valiev@pnl.gov<br>
&nbsp;</span><span style=3D'color:blue'> </span><span =
style=3D'font-size:14.0pt;
font-family:"Arial","sans-serif";color:blue'><o:p></o:p></span></p>

<div>

<div style=3D'border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt =
0in 0in 0in'>

<p class=3DMsoNormal><b><span =
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span>=
</b><span
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Mark =
Cunningham
[mailto:cunningham@utpa.edu] <br>
<b>Sent:</b> Friday, July 06, 2007 12:18 PM<br>
<b>To:</b> Valiev, Marat<br>
<b>Subject:</b> RE: [NWCHEM] QM/MM geometry =
constraints<o:p></o:p></span></p>

</div>

</div>

<p class=3DMsoNormal><o:p>&nbsp;</o:p></p>

<div id=3DidOWAReplyText22786>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>Dr. Valiev:</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>I
am interested in constraining the distance between two atoms =
in</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>the
quantum partition.&nbsp; Must I place an harmonic restraint on the =
</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>atoms?&nbsp;
</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>I
thought that the QM/MM code invoked the standard</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>QM
utilities to compute energies and the like and that =
NWChem</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>used
internal coordinate representations internally.&nbsp; Is =
there</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>some
way to (manually) force an internal coordinate in =
the</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>QM
part of a QM/MM calculation?&nbsp; I could/would modify =
the</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>appropriate
code if you can point me in the proper direction.</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>Thanks
for your help</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>Mark
Cunningham</span><o:p></o:p></p>

</div>

</div>

<div>

<p class=3DMsoNormal><o:p>&nbsp;</o:p></p>

<div class=3DMsoNormal align=3Dcenter style=3D'text-align:center'>

<hr size=3D3 width=3D"100%" align=3Dcenter>

</div>

<p class=3DMsoNormal style=3D'margin-bottom:12.0pt'><b><span =
style=3D'font-size:10.0pt;
font-family:"Tahoma","sans-serif"'>From:</span></b><span =
style=3D'font-size:10.0pt;
font-family:"Tahoma","sans-serif"'> Valiev, Marat =
[mailto:marat.valiev@pnl.gov]<br>
<b>Sent:</b> Fri 7/6/2007 11:49 AM<br>
<b>To:</b> Mark Cunningham; nwchem-users@emsl.pnl.gov<br>
<b>Subject:</b> RE: [NWCHEM] QM/MM geometry =
constraints</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>Mark,</span><o:p></o:p></p>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>QM/MM module does not use internal coordinates =
representation, thus
your errors.</span><o:p></o:p></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>Also aside the potential use, the actual charmm fragment =
files have
never been tested.</span><o:p></o:p></p>

<p class=3DMsoNormal><span =
style=3D'font-size:14.0pt;font-family:"Arial","sans-serif";
color:blue'>I would recommend using AMBER force =
field.</span><o:p></o:p></p>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

<p class=3DMsoNormal style=3D'margin-bottom:12.0pt'><span =
style=3D'font-size:10.0pt;
color:blue'>Marat Valiev, Ph.D.<br>
Senior Research Scientist<br>
Molecular Sciences Software Group (NWChem)<br>
marat.valiev@pnl.gov</span><o:p></o:p></p>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;color:blue'>&nbsp;</span><span
style=3D'color:blue'> </span><o:p></o:p></p>

<div>

<div style=3D'border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt =
0in 0in 0in'>

<p class=3DMsoNormal><b><span =
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span>=
</b><span
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
owner-nwchem-users@emsl.pnl.gov [mailto:owner-nwchem-users@emsl.pnl.gov] =
<b>On
Behalf Of </b>Mark Cunningham<br>
<b>Sent:</b> Thursday, July 05, 2007 1:40 PM<br>
<b>To:</b> nwchem-users@emsl.pnl.gov<br>
<b>Subject:</b> [NWCHEM] QM/MM geometry =
constraints</span><o:p></o:p></p>

</div>

</div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif";
color:black'>I am trying to use NWChem 5.0 to perform QM/MM calculations =
but my
progress</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>has
been hampered by the fact that none of the examples in the =
distribution</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>actually
run.&nbsp; Additionally, it appears that all of the CHARMM fragment =
files are</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>incorrect.</s=
pan><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>My
problem at the moment is to specify a geometry constraint.&nbsp; In an =
all QM</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>calculation,
I can use zcoord&nbsp;to force&nbsp;an atom-atom distance to be some =
value</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>without
having to use an harmonic restraint.&nbsp; In&nbsp;a QM/MM calculation, =
I tried
using </span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>the
same strategy: after task prepare, I specified:</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>geometry<br>
&nbsp;&nbsp; zcoord<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; bond 77 153 3.5 constant<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; torsion 69 71 77 153 178.12 constant<br>
&nbsp;&nbsp; end<br>
end</span><o:p></o:p></p>

</div>

<p><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>This results
in the following error:</span><o:p></o:p></p>

<p><span style=3D'font-size:10.0pt;font-family:"Courier New"'>User =
specification
of redundant internal variables<br>
&nbsp;--------------------------------------------------</span><o:p></o:p=
></p>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>&nbsp;&nbsp;
i&nbsp;&nbsp; j&nbsp;&nbsp; k&nbsp;&nbsp; l&nbsp;&nbsp;&nbsp;&nbsp;
value&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; name&nbsp;&nbsp; frz<br>
&nbsp; --- --- --- --- ------------ -------- ---<br>
&nbsp;&nbsp; 77
153&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;
3.500000 User001&nbsp;&nbsp;&nbsp; T<br>
&nbsp;&nbsp; 69&nbsp; 71&nbsp; 77 153&nbsp;&nbsp; 178.120000
User002&nbsp;&nbsp;&nbsp; T</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span style=3D'font-size:10.0pt'><br>
</span><span style=3D'font-size:10.0pt;font-family:"Courier =
New"'>&nbsp;Scaling
coordinates for geometry &quot;geometry&quot; by&nbsp; 1.889725989<br>
&nbsp;(inverse scale =3D&nbsp; 0.529177249)</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Courier New"'>&nbsp;
geom_cart_set: too many
centers&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
0 geometry<br>
&nbsp; geom_masses_set: too many
centers&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
0 geometry<br>
&nbsp; geom_nucexps_set: too many
centers&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
0 geometry<br>
&nbsp;-------------------------------------------------------------------=
-----<br>
&nbsp;geom_input: geom_nucexps_set
failed&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0<br>
&nbsp;-------------------------------------------------------------------=
-----<br>
&nbsp;-------------------------------------------------------------------=
-----<br>
&nbsp; current input line :<br>
&nbsp;&nbsp;&nbsp; 42: end<br>
&nbsp;-------------------------------------------------------------------=
-----</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>I
would appreciate any advice.</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>Mark
A Cunningham</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>The
University of Texas-Pan American</span><o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

</div>

</div>

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