[gmx-users] LIGAND TOPOLOGY

[MUSYOKA THOMMAS]

Dear users,
I have been trying to build la ligand topology of my ligand through the
PRODRG web server.
I have the following queries;
According to Justin's important tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
i am lost on how to allocate equivalent charges to equivalent groups. I
have read the recommended paper but seems still i have issues in allocating
the correct charges to my groups.

Secondly, its about how to determine which groups are encompassed by a
charge group

Attached find in my PRODRG input file.
Someone out there help me in understanding this.
Thanks in advance.
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html>--

*MUSYOKA THOMMAS MUTEMI
Mob nos **+27844846540**
B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science
(Nagasaki University)*
*PhD Student-Bioinformatics (Rhodes University)
*Skype ID- MUSYOKA THOMMAS MUTEMI
Alternative email - thommas at sia.co.ke
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