[gmx-users] Error in .top when running grompp for final product MD

[한상화]

Dear gromacs users,

 

I am running MD for a protein with 212 amino acid residues.

When I run grompp (grompp -f pn_md.mdp -c pn_md.pdb -r pn_md.pdb -p pn.top -
o pn_md.tpr ) for the final product MD, I receive the following error
message.

I properly included sol and ion in the temperature control part of
pn_md.mdp.

If I include “define = -DPORRES” in pn_md.mdp, both grompp and mdrun work
fine.

The topolofy file pn.top worked well in the previous steps (em.mdp and
pr.mdp).

Any suggestions would be appreciated.

 

Sanghwa Han

 

[Error Message]

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 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.4#
checking input for internal consistency...
....ling /usr/bin/cpp 
: no such file or directory
cpp: warning: '-x c' after last input file has no effect
cpp: no input files
cpp exit code: 256
  -I/usr/local/gromacs/share/gromacs/top  pn.top > gromppcHKNXc'
' 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 (pn_md.pdb, 34158)
             does not match topology (pn.top, 0)
-------------------------------------------------------

 

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