On 27/10/2011 12:28 AM, Atila Petrosian wrote:
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"
This is the kind of thing to which I was referring, but it appears you
have edited your .top and removed the #endif lines that should match the
#ifdef. Start again with pdb2gmx to generate a new .top, and then you
will be able to choose your "define = -DPOSRES_xxx" to use position
restraints on whichever part of the system you want with no need to ever
touch a .top or .itp file.
Mark
; 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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