[gmx-users] grompp error in running simultion of membrane protein with lipid bilayer

nitu sharma sharmanitu35 at gmail.com
Fri Apr 3 08:18:51 CEST 2009

Dear all,

                   I am trying to do simulation of membrane protein with
lipid bilayer  for this I have made topology file like this-
; topology for tap in 128 dmpc lipids plus water.
; rr1_A.itp and rr1_B.itp can be made in a straightforward manner with
pdb2gmx, starting
; with a pdb file of tap transporter.
; make sure lipid.itp,dmpc.itp and rr1.itp are in a location where
; grompp can find them (GMXLIB, current directory, or directory given in
; the .mdp file with the include option.
#include "ffoplsaa.itp"
#include "lipid.itp"
#include "dmpc.itp"

; Include chain topologies
#include "rr1_A.itp"
#include "rr1_B.itp"

;#ifdef POSRES
;#include "posre_A.itp"
;#include "posre_B.itp"
;#include "lipid_posre.itp"
; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"

[ system ]
; Name

[ molecules ]
; compound  #mols
Protein_A    1
Protein_B    1
DMPC        128
;SOL        3551

SOL             24020
SOL             43676

when I am trying to run grompp after solvating the system I am getting error
like this-
Program grompp, VERSION 4.0.3
Source code file: toppush.c, line: 843

Fatal error:
Atomtype C not found
my command  line like this-
grompp -f em.mdp -p rr1-dmpc.top -c solvated-tapp-mod.pdb -o tapp-mod-em.tpr
 if anyone know about this please suggest me right thing to do.

Nitu Sharma
School of life sciences
Jawaherlal Nehru University
New Delhi India
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