[gmx-users] Re: Problem: pdb2gmx with a more complex system

Jernej Zidar jernej.zidar at gmail.com
Tue Mar 27 10:15:46 CEST 2012

Dear Mark and Justin,
  Thank you for the clarification. Running the pdb2gmx with the
following switches was enough to get a working topology file: pdb2gmx
-v -f sys9-tmp.pdb -water spc -noter -o sys9-tmp.gro -p sys9-tmp.top
-i sys9-tmp.itp -renum

  The resulting topology file is very simple:
; Include forcefield parameters
#include "./charmm36cgenff.ff/forcefield.itp"

; Include chain topologies
#include "sys9-tmp-polymer.itp"

; Include Position restraint file for polymer
#ifdef POSRES
#include "sys9-tmp-polymer-pr.itp"

#include "sys9-tmp-lipid.itp"

; Include Position restraint file for lipids
#ifdef POSRES
#include "sys9-tmp-lipid-pr.itp"

; Include water topology
#include "./charmm36cgenff.ff/spc.itp"
; Include topology for ions
#include "./charmm36cgenff.ff/ions.itp"

[ system ]
; Name
Polymer and lipid bilayer in water

[ molecules ]
; Compound        #mols
LIPID       1
SOL         2295
CL          2

  Thanks for the explanations for I understood that one needs to
specify the exact number of molecules in the [ molecules ] section,
though it seems that's not neccessarily the case as both Justin and
Mark pointed out.

  I also noticed the unit cell size gets properly detected and written
at the end of the GRO file.


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