[gmx-users] Topology file

Ankita naithani ankitanaithani at gmail.com
Wed Aug 15 15:05:55 CEST 2012


I noticed that in my topology file, there is no inclusion of position
restraint file for my protein. For instance, my topology file looks
like this:

; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_D.itp"
#include "topol_Protein_chain_E.itp"
#include "topol_Protein_chain_F.itp"
#include "topol_Protein_chain_G.itp"

;Include ligand topology
#include "FDP_Dp.itp"

; Include water topology
#include "gromos53a6.ff/spc.itp"

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

; Include topology for ions
#include "gromos53a6.ff/ions.itp"

But, after running pdb2gmx, I do get 4 posre files for all the
individual chains. Do I need to add in them manually? Also, I am
unable to understand as to why did it not get included in the first
instance itself? I am using gromos53a6 force field.

Best Wishes,

Ankita Naithani

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