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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