[gmx-users] position restrained minimization on the one part of a system

Atila Petrosian atila.petrosian at gmail.com
Wed Oct 26 15:28:53 CEST 2011

Dear Mark

thanks for your reply

you said "if pdb2gmx is able to treat the whole system in one pass, then it
will write such position restraint
files automatically"

in my system, what pdb2gmx includes are in below:

; Include forcefield parameters
#include "amber03.ff/forcefield.itp"

; Include chain topologies
#include "complex_Protein_chain_A.itp"
#include "complex_DNA_chain_B.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre_Protein_chain_A.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre_Protein_chain_B.itp"

; Include water topology
#include "amber03.ff/tip3p.itp"

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

; Include topology for ions
#include "amber03.ff/ions.itp"

[ system ]
; Name

[ molecules ]
; Compound        #mols
Protein_chain_A     1
DNA_chain_B         1
SOL                        3500

unfortunately, I don't know about step 1.

please guide me about that.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111026/d5541f06/attachment.html>

More information about the gromacs.org_gmx-users mailing list