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

[Atila Petrosian]

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"

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

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

[ system ]
; Name
complex

[ 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.
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