[gmx-users] adding hydrogens to protein with pdb2gmx

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Wed Sep 5 11:05:18 CEST 2012

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/*
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list