[gmx-users] topology file in DPPC

scaprari at uniroma3.it scaprari at uniroma3.it
Tue May 15 16:47:52 CEST 2012

Dear all,
I'm meticulously following the tutorial KALP-15 in DPPC in order to carry
on the simulation of a protein of mine in a extended patch of DPPC. I have
already modified the ffnonbonded.itp and ffbonded.itp. At this point I'm
reading that I should change my topology file but I'm not able to find
within my topology file (obtained by using pdb2gmx on my protein)
#include"gromos53a6.ff/forcefield.itp"statement so as to replace this line
with #include "gromos53a6_lipid.ff/forcefield.itp", as reported in the
Indeed, at the top of my topology file I have got;

; Include forcefield parameters
#include "ffG53a6.itp"

and, after the list of all atoms,  at the bottom of the file;

; Include Position restraint file
#ifdef POSRES
#include "posre.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

[ molecules ]
; Compound        #mols
Protein_A           1

I'm wondering if it may depend on the fact I have got the version  
gromacs-4.0.7 and not the version 4.5.3 or newer or if I have to change
some options when I launch the command pdb2gmx in order to build my
topology file. I used the following command:

pdb2gmx -f 3G8G.pdb -o 3G8G_membr.gro  -p 3G8G_membr.top  -i
3G8G_membr.itp -ignh -water spc

and I chose GROMOS96 53A6

Please, let me know.


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