[gmx-users] sridhar: How to include topologies for unusual/phosphorylated residues occurring within the protein chain.

David van der Spoel spoel at xray.bmc.uu.se
Fri May 16 09:01:01 CEST 2003

On Fri, 2003-05-16 at 18:14, Mr.Sridhar wrote:
> Dear Gromacs users,
> I am a graduate student at Centre for DNA Fingerprinting and Diagnostics,
> Hyderabad, India. I am currently working on Dynamic simulation studies
> using GROMACS software.
> In my current work I want to do simulation of a protein containing
> PhosphoSerine. Regarding this I went through the Article "Gromacs Tutorial
> for Drug-Enzyme Complex" which has shown clearly step-by-step how to
> include new topologies for drug/ligand molecules.
> By I was not successful in running the dynamics. I got topology for
> Phosphoserine from PRODRG server. The "Drug-Enzyme complex" tutorial was
> specific for ligands/Drugs that do not form part of the protein chain. But
> if I want to include topology for special residues like Phosphoserine
> which occur within the protein chain, how to do it?
> I tried according to the tutorial but was unsuccessful all the time.
> I'll be very grateful if you can outline me the procedure to be
> followed in such cases.
You have to make a new entry in the .rtp file (and a corresponding .hdb
entry). I have a vague rrecollection that it has been covered on the
mailing list... YEs, search for it on the website

> Thankyou very much.
> sridhar.
> On Sat, 10 May 2003, Mr.Sridhar wrote:
> >
> >
> >
> >
> >
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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