[gmx-users] simulation with ligand at the active site

Aldo Segura asegurac666 at yahoo.com.mx
Thu Apr 28 16:18:07 CEST 2011

something like happened to me, the solution that worked for me was to use acpype
(code.google.com/p/acpype) and Amber FF. In this way, you could rule out
problems related to the prodrg parameters.


Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747
e-mail: asegurac at ipn.mxaldosegura at gmail.com

--- El jue 28-abr-11, Justin A. Lemkul <jalemkul at vt.edu> escribió:

De: Justin A. Lemkul <jalemkul at vt.edu>
Asunto: Re: [gmx-users] simulation with ligand at the active site
A: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Fecha: jueves, 28 de abril de 2011, 1:02

onetwo wrote:
> Hello Users,
> I have a query regarding simulation with the ligand.
> In my protein there are two ligands, one of them (coenzyme) is from the
> crystal data, and other I have docked at the active site, while docking
> it is showing good interaction with all the active site residues very
> well.
> I used GROMOS96 43a1 force field, and got the topology file made from
> prodrg beta, using GROMOS 96.1 for both the ligands.

PRODRG produces notoriously bad topologies.  See, for instance:


> while doing equilibration I did, brendenson coupling on like
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = V-rescale
> tc-grps = Protein Non-Protein
> tau_t = 0.1 0.1
> ref_t = 300 300
> and in MD simulation also
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = V-rescale
> tc-grps = Protein Non-Protein
> tau_t = 0.1 0.1
> ref_t = 300 300

There could be some debate about these settings, and I do not know the best way to handle temperature coupling.  It seems to me that if you have a ligand (or multiple) bound to a protein, the interactions between the protein and ligand(s) will be tightly coupled, such that you shouldn't lump the ligands into the "Non-Protein" group, which in this case likely comprises solvent.  Maybe someone with more experience in these types of simulations can share some insight.

> But after 1ns equibiration, one of the ligand (the one which I docked)
> is going away from the active site and then I ran it for 4 ns further,
> it has gone more far from the cavity. Following is the link to the snapshot of the ligand at different time.
> https://picasaweb.google.com/118389174994698260649/Md_complex?authkey=Gv1sRgCMis2qry3cGj7AE#5600499037480314402
> I want to ask if the change in the
> position of ligand is justified with the parameters i have taken or it
> if i have done something wrong?

Without providing the actual topology(ies) of the ligand(s) and a complete .mdp file, it is hard to say.  But if you're using PRODRG output, I would suspect that it would be the culprit.


> Thanks and Regards
> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle?>

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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