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 - thom...@sia.co.ke * "Do all the good you can, By all the means you can, In all the ways you can, In all the places you can, At all the times you can, To all the people you can, As long as ever you can." - John Wesley. *
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