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

Leonardo Sepulveda Durán leonardosepulveda at gmail.com
Thu Dec 1 14:58:28 CET 2005


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.


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