[gmx-users] adding hydrogens to protein with pdb2gmx

[reisingere at rostlab.informatik.tu-muenchen.de]

Hi Marcelo,
thanks a lot for your help!!

> After doing the 'pdb2gmx', created the cell e filled with solvent, use the
> "make_ndx" to create an index of your system. One of the groups should be
> your residues that you want to freeze. Then, in your .mdp file, use
> 'freezegrps' and 'freezedim' in your recently created group.
>
> Don't forget the -n yourindexfile.ndx in the grompp command line. It
> should
> work.
> Good luck!
> --
> Marcelo Depólo Polêto
> Bolsista FAPEMIG
> Laboratório de Infectologia Molecular Animal - LIMA
> Departamento de Bioquímica e Biologia Molecular
> Universidade Federal de Viçosa - UFV
> Tel.: +55 31 3899-2911/2912
> MSN: marcelodepolo at gmail.com <marcelodepollo at hotmail.com>
> *Website: http://opensourcebioinformatics.com/site/*
> --
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