[gmx-users] determining restraints for pulling

[Mark Abraham]

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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