[gmx-users] Convert A CHARMM pdb file to gromacs

Maik Goette mgoette at mpi-bpc.mpg.de
Mon Dec 5 15:20:27 CET 2005


First: I don't know CHARMM...and maybe I'm lucky with that...;)

I think, CHARMM writes out "wrong" hydrogen names.
You have to rename all hydrogens according to GROMACS nomenclature.
Maybe there is something in the manual about that.
If not, scan the RTP file for that.
IMHO thats the only way to keep your hydrogens.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Leonardo Sepulveda Durán wrote:
> Hello!!!
> I have a Solvated system protuced by CHARMM, in pdb format. (with hydrogens)
> I would like to use this same system in GROMACS, to compare without
> having a different initial structure. Using
> pdb2gmx  -f S1.pdb
> Gives an error because the TIP3 waters and Protein Hydrogens can not
> being recognized. Adding the -ignh option changues every hidrogen
> position, for water and oxigen.
> I would like to know if someone knows a program or script to convert
> CHARMM hydrogen  names into GROMACS (encad) ones.
> Leonardo
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