[gmx-users] PRODRG2 output-why only polar hydrogens?

A. A. Jeyaprakash jprakash at mbu.iisc.ernet.in
Wed Jul 14 13:25:58 CEST 2004

Dear Gromacs Users,

       I generated the topology file for my ligand using PRODRG2 server.  
DRGFIN.GRO and DRGGMX.ITP files contain only polar hydrogens. Why is
that so? is it not necessary to include all the hydrogens of the ligand
during the MD on GROMACS?

       Thanks in advance,

with regards,

A. Arockia Jeyaprakash, 
Research Associate, Molecular Biophysics Unit,Indian Institute of Science, 
Bangalore-560 012 INDIA
Ph: +91-80-22932389 Fax:+91-80-23600535

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