[gmx-users] determining restraints for pulling

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 4/5/17 8:04 AM, abhisek Mondal wrote:
> Hello Justin,
>
> Can you provide some direction to this approach I'm using for performing
> umbrella sampling of a protein-ligand complex ?
>
> 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.
>
> Some suggestions regarding the issue will be highly appreciated.
>

What does your examination of the literature for similar systems suggest as an 
appropriate protocol?

-Justin

> Thank you
>
> On Wed, Apr 5, 2017 at 3:51 PM, abhisek Mondal <abhisek.mndl at gmail.com
> <mailto:abhisek.mndl at gmail.com>> wrote:
>
>     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
>     <mailto: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
>         <mailto: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
>     /
>
>
>
>
> --
> Abhisek Mondal
> /Senior Research Fellow
> /
> /Structural Biology and Bioinformatics Division
> /
> /CSIR-Indian Institute of Chemical Biology/
> /Kolkata 700032
> /
> /INDIA
> /

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================