[gmx-users] problem in topology file for protein+lipid bilayer system

nitu sharma sharmanitu35 at gmail.com
Sat Apr 4 08:55:45 CEST 2009

Hello justin

thanks for ur suggestion . I am trying to do membrane protein simulation
with lipid bilayer . I have pdb file of inserted protein in dmpc lipid
bilayer. But I am facing problem in making topology file for this system.As
u told in previous mail you can't combine OPLS_AA with a standerd berger
lipid parameter right but   even if I used the force field ffgmx  than also
I am getting error

my topology file like this which I have made-

topology for 1 protein molecule in 128 dmpc lipids, water and 1 counter ion.
; rr1_A.itp and rr1_B.itp can be made in a straightforward manner with
; 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 forcefield parameters
#include "ffgmx.itp"
#include "lipid.itp"
#include "dmpc.itp"

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

; Include position restrain protein
;#include "posre_A.itp"
;#include "posre_B.itp"
; Include position restrain lipid
;#include "lip_posre.itp

; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"

;Position restraint for each water oxygen
[ position_restraints ]
; i funct  fcx      fcy      fcz
  1  1     1000     1000     1000

; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name

[ molecules ]
; compound  #mols
Protein_A    1
Protein_B    1
DMPC        128
SOL        3552
Na           1

*and the error I am getting like this-

processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxbon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 1369 of the 2211 non-bonded parameter combinations

Program grompp, VERSION 4.0.3
Source code file: toppush.c, line: 947

Fatal error:
Atomtype opls_287 not found
can u please suggest me is their any error in topology file and where should
I have to make chnge.
If I want to use ffgmx force field.
as like if I want to use oplsaa  force field I have to make change in

please suggest me what should I have to do if I am using ffgmx force field.

Thanks a lot in advance.
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