[gmx-users] protein insertion

mahbubeh zarrabi zarrab_m at yahoo.com
Mon May 1 14:08:41 CEST 2006

Dear freinds
  There are some errors when I run grompp.
  I try to use make_hole program to make a hole in
  ./make_hole.pl -f popc128a.pdb -o popc.pdb -r 1.4
-lipat P8 -lipid POPC -cx 2.3 -cy 2.8 
  editconf -f popc.pdb -o popc.gro
  editconf -bt cubic -f popc.gro -o popc.gro -c -d 0.5
  genbox -cp popc.gro -cs spc216.gro -o popc_b4em.gro
-p popc.top
  This is my popc.top after genbox.
#include "ffgmx_lipid.itp"
#include "popc.itp"
;#include "ions.itp"

#ifdef POSRES
#include "lipid_posre.itp"

#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"

[ system ]
; name
popc + h2o

[ molecules ]
; name	number
POPC   106 

There is my em.mdp file.
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
nsteps              =  100
;	Energy minimizing stuff
emtol               =  2000
emstep              =  0.01

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no

grompp -f em.mdp -c popc_b4em.gro -p popc.top -o

After doing these, error message is appeare:

popc.top:1:27: error: ffgmx_lipid.itp: No such file or
popc.top:2:20: error: popc.itp: No such file or
cpp exit code: 256
Tried to execute: '/lib/cpp 
-I/usr/local/gromacs/share/top -DFLEX_SPC popc.top >
The '/lib/cpp' command is defined in the .mdp file
processing topology...
Cleaning up temporary file gromppzaUDO1
Program grompp, VERSION 3.3.1
Source code file: topio.c, line: 388

Fatal error:
Invalid order for directive moleculetype, file
""/usr/local/gromacs/share/top/flexspc.itp"", line 1
best regard

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