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

[Tsjerk Wassenaar]

Hi Vivek,

Either

1. Use the original ligand coordinates with the PRODRG topology

or

2. Fit the structure obtained from PRODRG to the original structure

Cheers,

Tsjerk

On Wed, Jan 27, 2010 at 5:58 AM, vivek sharma
<viveksharma.iitb at gmail.com> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist