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

nitu sharma sharmanitu35 at gmail.com
Thu Apr 23 07:01:10 CEST 2009

Dear Justin

                            I am doing simulation of membrane protein .I
follow your tutorial for that I think its perfect for that. But I am getting
problem in doing inflategro step, I alredy discuss this problem with you but
now I am starting everything fresh  I have completed upto concatanation of
protein with lipid bilayer after that for packing of lipid around protein I
am using inflategro script from teleman website . Problem came in second
step of inflategro i.e for energy minimisation for this I need topology file
of "protein-lipid system".
I am giving you information in detail i.e -
for topology file I have made changes in topol.top file which I got from
pdb2gmx command in first step for protein processing ,the topol .top file is
like  this-
File 'topol.top' was generated
;       By user: nitu (504)
;       On host: localhost.localdomain
;       At date: Thu Apr 16 23:20:48 2009
;       This is your topology file
;       Grunge ROck MAChoS
; Include forcefield parameters
#include "ffG53a6.itp"

; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"

; Include water topology
#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
Grunge ROck MAChoS

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
And the change topology file is like this-

; Include forcefield parameters
#include "ffG53a6_lipid.itp"

; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"

#ifdef POSRES
#include "posre_A.itp"
#include "posre_B.itp"

; Include DMPC chain topology
#include "dmpc.itp"

[ system ]
; Name
Protein in DMPC bilayer

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
DMPC               128

but when I gave this topology file to grompp it shws error-
no. of coordinates in coordinate file doesn,t mach the topology file .

Can you suggest me something for making topology file for protein-lipid
bilayer system. Is there any other method for making topology file ,I have
read in mannual chapter 5 but there is also mentioned same method.
If possible please help me becoz without solving this problem I can't move
for furthur processing .

* My gro file of protein shows 9902 atoms .
As you ask in previous mail is .itp file have [ molecules ] section the
answer is the .itp file haven't molecules section it have [molecule type ]
section can it also create problem for topology file working.

 Thanks a lot justin .
I am waiting for your reply.

Nitu sharma
School of life sciences
Jawaherlal Nehru University
New delhi , India
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