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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:blue'>Hi Priya;<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:blue'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:blue'>I had this problem with Windows version (never tried Linux one),
coz the output file is not generated (renamed in code) properly.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:blue'>I suggest, you run the demo script (to test again) and if still you
are getting the error, then you have to modify the code (I solved this problem
this way).<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:blue'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:8.0pt;color:#4BACC6'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif";
color:#4BACC6'>Thank You;<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Tahoma","sans-serif";
color:#4BACC6'>URPradhan At Gmail Dot Com<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:blue'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>priya priya<br>
<b>Sent:</b> Tuesday, July 03, 2007 5:31 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] error running position restraints<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal style='margin-bottom:12.0pt'>hi all, <br>
<br>
i have installed Gromacs and tried running simulation using explicit solvent.i
did pdb2gmx to convert my pdb file to gromacs coordinate file and then editconf
and genbox to add water molecules.<br>
next i did minimization it run well but when i tried to run position restraints
i have to face an error:<br>
My commnd: <br>
grompp -f gr15-42_wat_md_prest.mdp -c 2bp_wat_emin_nic.gro -p 2bp_nic.top -o
2bp_wat_md_prest_nic.tpr<br>
<br>
out error:<br>
<br>
creating statusfile for 1 node...<br>
' for variable integrator, using 'md'<br>
Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'<br>
' for variable ns-type, using 'Grid'<br>
Next time use one of: 'Grid' 'Simple'<br>
' for variable coulombtype, using 'Cut-off'<br>
Next time use one of: 'Cut-off' 'Reaction-Field' 'Generalized-Reaction-Field'
'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift' 'User' 'Generalized-Born'
'Reaction-Field-nec' 'Encad-shift' 'PME-User'<br>
' for variable optimize_fft, using 'no'<br>
Next time use one of: 'no' 'yes'<br>
' for variable tcoupl, using 'No'<br>
Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen'
'Andersen-interval'<br>
' for variable Pcoupl, using 'No'<br>
Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'<br>
' for variable Pcoupltype, using 'Isotropic'<br>
Next time use one of: 'Isotropic' 'Semiisotropic' 'Anisotropic'
'Surface-Tension'<br>
' for variable gen-vel, using 'no'<br>
Next time use one of: 'no' 'yes'<br>
' for variable constraints, using 'none'<br>
Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'<br>
<br>
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18#<br>
checking input for internal consistency...<br>
...ling /usr/bin/cpp/<br>
: Not a directory<br>
cpp exit code: 32256<br>
-I/usr/local/gromacs/share/gromacs/top 2bp_nic.top >
grompp7ynGtl'<br>
' command is defined in the .mdp file<br>
processing topology...<br>
processing coordinates...<br>
-------------------------------------------------------<br>
Program grompp, VERSION 3.3.1<br>
Source code file: grompp.c, line: 448<br>
<br>
Fatal error:<br>
number of coordinates in coordinate file (2bp_wat_emin_nic.gro, 6544)<br>
does
not match topology (2bp_nic.top, 0)<br>
<br>
I have checked the Top file it has spc.itp included in it, i have even tried to
create top file from the gro file created by running minimization but still the
same error.if one want to see my Mdp file i can send that also.<br>
<br>
Regards<br>
-------------------------------------------------------<br>
<br>
<o:p></o:p></p>
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