[gmx-users] error running position restraints

[Utkal Ranjan Pradhan]

Hi Priya;

 

I had this problem with Windows version (never tried Linux one), coz the
output file is not generated (renamed in code) properly.

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).

 

 

Thank You;

URPradhan At Gmail Dot Com

 

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of priya priya
Sent: Tuesday, July 03, 2007 5:31 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] error running position restraints

 

hi all, 

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.
next i did minimization it run well but when i tried to run position
restraints i have to face an error:
My commnd: 
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
                        
out error:

creating statusfile for 1 node...
' for variable integrator, using 'md'
Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'
' for variable ns-type, using 'Grid'
Next time use one of: 'Grid' 'Simple'
' for variable coulombtype, using 'Cut-off'
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'
' for variable optimize_fft, using 'no'
Next time use one of: 'no' 'yes'
' for variable tcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen'
'Andersen-interval'
' for variable Pcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'
' for variable Pcoupltype, using 'Isotropic'
Next time use one of: 'Isotropic' 'Semiisotropic' 'Anisotropic'
'Surface-Tension'
' for variable gen-vel, using 'no'
Next time use one of: 'no' 'yes'
' for variable constraints, using 'none'
Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18#
checking input for internal consistency...
...ling /usr/bin/cpp/
: Not a directory
cpp exit code: 32256
  -I/usr/local/gromacs/share/gromacs/top  2bp_nic.top > grompp7ynGtl'
' command is defined in the .mdp file
processing topology...
processing coordinates...
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (2bp_wat_emin_nic.gro, 6544)
             does not match topology (2bp_nic.top, 0)

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.

Regards
-------------------------------------------------------



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