[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
tutorial.
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"
#endif
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
PHOSPHOLIPASE A2, AMMODYTOXIN A
[ 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.
Silvia
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