Hi Tsjerk,<br>Thanks for your response, <br>I am finding problem in using original coordinates with the PRODRG topology because of mismatch in number of Hydrogen atoms in original coordinate file and PRODRG topology.<br>Can you tell me how can I try 2nd option you suggested i.e. Fit the structure obtained from PRODRG to original structure?<br>
<br>Thanks & Regards,<br>Vivek<br><br><div class="gmail_quote">On 27 January 2010 10:35, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Vivek,<br>
<br>
Either<br>
<br>
1. Use the original ligand coordinates with the PRODRG topology<br>
<br>
or<br>
<br>
2. Fit the structure obtained from PRODRG to the original structure<br>
<br>
Cheers,<br>
<font color="#888888"><br>
Tsjerk<br>
</font><div><div></div><div class="h5"><br>
On Wed, Jan 27, 2010 at 5:58 AM, vivek sharma<br>
<<a href="mailto:viveksharma.iitb@gmail.com">viveksharma.iitb@gmail.com</a>> wrote:<br>
> Hi Dallas,<br>
> I am trying to run MD simulation over a docked complex (protein+ligand), to<br>
> confirm their dynamic stability in water media.<br>
> For the same I am using PRODRG server to generate topologies for ligand<br>
> molecule as gromacs can generate topology for 20 standard residues. As<br>
> mentioned in tutorial for drug-enzyme complex, I am editing the .top and<br>
> .gro files to include the PRODRG generated files (DRGGMX.ITP in .top and<br>
> DRGAPH.GRO in .gro file).<br>
> I observe that their are changes in co-ordinate of ligand after processing<br>
> them through PRODRG server. So these new co-ordinates for ligand are placing<br>
> ligand away from the protein while the ligand molecule was in protein pocket<br>
> in original docked complex.<br>
><br>
> I hope it gives what I am trying to do, and where I am getting stuck.<br>
><br>
> I am looking for some suggestions and more insight of the problem to solve<br>
> it.<br>
> Earlier I have done same procedure successfully for a different docked<br>
> complex.<br>
><br>
> Regards,<br>
> Vivek<br>
><br>
> 2010/1/27 Dallas B. Warren <<a href="mailto:Dallas.Warren@pharm.monash.edu.au">Dallas.Warren@pharm.monash.edu.au</a>><br>
>><br>
>> So, what EXACTLY are you doing?<br>
>><br>
>><br>
>><br>
>> Catch ya,<br>
>><br>
>> Dr. Dallas Warren<br>
>> Drug Delivery, Disposition and Dynamics<br>
>> Monash Institute of Pharmaceutical Sciences, Monash University<br>
>> 381 Royal Parade, Parkville VIC 3010<br>
>> <a href="mailto:dallas.warren@pharm.monash.edu.au">dallas.warren@pharm.monash.edu.au</a><br>
>> +61 3 9903 9167<br>
>> ---------------------------------<br>
>> When the only tool you own is a hammer, every problem begins to resemble a<br>
>> nail.<br>
>><br>
>><br>
>><br>
>> From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>]<br>
>> On Behalf Of vivek sharma<br>
>> Sent: Monday, 25 January 2010 7:38 PM<br>
>> To: Discussion list for GROMACS users<br>
>> Subject: Re: [gmx-users] Ligand coming out while trying Drug-enzyme<br>
>> tutorial<br>
>><br>
>><br>
>><br>
>> HI Tsjerk,<br>
>><br>
>> Thanks for your reply. But, I can't see if it is going suddenly or<br>
>> gradually.<br>
>> What i can see is the ligand is away from the molecule after editing the<br>
>> gro file with PRODRG output.<br>
>><br>
>> It seems liek PRODRG has modified the co-ordinates that places ligand away<br>
>> from the protein.<br>
>><br>
>> ~Vivek<br>
>><br>
>> 2010/1/25 Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
>><br>
>> Hi Vivek,<br>
>><br>
>> > Now when I am processing the modified .gro file to generate box, the<br>
>> > ligand<br>
>> > and cofactor are going away from the protein molecule and I am not able<br>
>> > to<br>
>> > analyze the complex.<br>
>><br>
>> Gradually going away, or suddenly jumping?<br>
>><br>
>> In the latter case, read up on periodic boundary conditions.<br>
>><br>
>> Tsjerk<br>
>><br>
>> --<br>
>> Tsjerk A. Wassenaar, Ph.D.<br>
>><br>
>> Computational Chemist<br>
>> Medicinal Chemist<br>
>> Neuropharmacologist<br>
>> --<br>
>><br>
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><br>
><br>
> --<br>
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><br>
<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
Computational Chemist<br>
Medicinal Chemist<br>
Neuropharmacologist<br>
--<br>
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</div></div></blockquote></div><br>