[gmx-users] determining restraints for pulling

[abhisek Mondal]

I had restrained it during the equilibration of the molecule. As advised in
the Protein-ligand simulation tutorial. But I'm unsure regarding what kind
of treatment I'm supposed to give the complex while targeting for umbrella
sampling. Do I need to restrain the ligand during equilibration ?

I have solved the crystal structure of the complex and want to determine if
I pull out the ligand then how the side chains reorient according to the
ligand withdrawal. That's the goal.

On Wed, Apr 5, 2017 at 3:09 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Why are you trying to keep the ligand in place (by restraining it) and pull
> it out?
>
> Mark
>
> On Wed, 5 Apr 2017 09:51 abhisek Mondal <abhisek.mndl at gmail.com> wrote:
>
> > Hi,
> >
> > 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"
> > #endif
> >
> > ; Include ligand topology
> > #include "drg.itp"
> >
> > ; Include position restraints
> > #ifdef POSRES_LIG
> > #include "posre_ACO.itp"
> > #endif
> >
> > ; 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*
> >
> > *INDIA*
> > --
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-- 
Abhisek Mondal

*Senior Research Fellow*

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

*Kolkata 700032*

*INDIA*