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

Mr.Sridhar sridhar at www.cdfd.org.in
Fri May 16 05:44:01 CEST 2003

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.

Thankyou very much.


On Sat, 10 May 2003, Mr.Sridhar wrote:


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