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

Nuno R. L. Ferreira nunolf at ci.uc.pt
Wed Jul 14 13:24:18 CEST 2004

----- Original Message ----- 
From: "A. A. Jeyaprakash" <jprakash at mbu.iisc.ernet.in>
To: <gmx-users at gromacs.org>
Sent: Wednesday, July 14, 2004 12:25 PM
Subject: [gmx-users] PRODRG2 output-why only polar hydrogens?

> 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?

Hi Jeyaprakash

Nope. Cause gromacs forcefield is not am all atom f.f., using only polar
hydrogens, as you saw in your files.
But, if you want to use an all atom f.f., you have the OPLS, which is also
implemented under gmx.

Best regards,

>        Thanks in advance,
> with regards,
> Jeyaprakash
> -- 
> 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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