[gmx-users] adding hydrogens to protein with pdb2gmx

Marcelo Depolo marcelodepolo at gmail.com
Tue Sep 4 18:09:18 CEST 2012

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
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/*

More information about the gromacs.org_gmx-users mailing list