[gmx-users] Ligand coming out while trying Drug-enzyme tutorial

[vivek sharma]

Hi Dallas,
I am trying to run MD simulation over a docked complex (protein+ligand), to
confirm their dynamic stability in water media.
For the same I am using PRODRG server to generate topologies for ligand
molecule as gromacs can generate topology for 20 standard residues. As
mentioned in tutorial for drug-enzyme complex, I am editing the .top and
.gro files to include the PRODRG generated files (DRGGMX.ITP in .top and
DRGAPH.GRO in .gro file).
I observe that their are changes in co-ordinate of ligand after processing
them through PRODRG server. So these new co-ordinates for ligand are placing
ligand away from the protein while the ligand molecule was in protein pocket
in original docked complex.

I hope it gives what I am trying to do, and where I am getting stuck.

I am looking for some suggestions and more insight of the problem to solve
it.
Earlier I have done same procedure successfully for a different docked
complex.

Regards,
Vivek

2010/1/27 Dallas B. Warren <Dallas.Warren at pharm.monash.edu.au>

>  So, what EXACTLY are you doing?
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at pharm.monash.edu.au
> +61 3 9903 9167
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>
> *From:* gmx-users-bounces at gromacs.org [mailto:
> gmx-users-bounces at gromacs.org] *On Behalf Of *vivek sharma
> *Sent:* Monday, 25 January 2010 7:38 PM
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] Ligand coming out while trying Drug-enzyme
> tutorial
>
>
>
> HI Tsjerk,
>
> Thanks for your reply. But, I can't see if it is going suddenly or
> gradually.
> What i can see is the ligand is away from the molecule after editing the
> gro file with PRODRG output.
>
> It seems liek PRODRG has modified the co-ordinates that places ligand away
> from the protein.
>
> ~Vivek
>
> 2010/1/25 Tsjerk Wassenaar <tsjerkw at gmail.com>
>
> Hi Vivek,
>
>
> > Now when I am processing the modified .gro file to generate box, the
> ligand
> > and cofactor are going away from the protein molecule and I am not able
> to
> > analyze the complex.
>
> Gradually going away, or suddenly jumping?
>
> In the latter case, read up on periodic boundary conditions.
>
> Tsjerk
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
>
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