[gmx-users] determining restraints for pulling

abhisek Mondal abhisek.mndl at gmail.com
Wed Apr 5 09:51:19 CEST 2017


I'm trying to pull a ligand from a protein-ligand complex. As per the
ligand-protein tutorial, I have restrained the ligand in topology file and
it looks like:

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

; Include ligand topology
#include "drg.itp"

; Include position restraints
#include "posre_ACO.itp"

; Include water topology
#include "gromos43a1.ff/spc.itp"

In the md_pull.mdp, I'm using:

title       = Umbrella pulling simulation
define      = -DPOSRES
; Run parameters
integrator  = md        ;applying leap frog algorithm

So, is it proper for pulling ligand (ACO) from the protein or I'm doing
something wrong ? I'm really lost here, please help me out.

Thank you.

Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*


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