[gmx-users] How to keep intact hdrogen coordinates from a PDB file

Nicolas SAPAY nsapay at ucalgary.ca
Wed Feb 28 01:40:25 CET 2007

Hello everybody,

I want to convert a .pdb file into a .gro using pdb2gmx but I have some
troubles with hydrogen coordinates : they are all modified by pdb2gmx
during the process. Actually, all hydrogens have been added previously
(with CHARMM), as well as the N- and C-terminal patches. When I give my
pdb file to pdb2gmx. all the coordinates of these atoms are (slighlty)
changed, according the rules defined in the .hdb and .tdb files, I guess.
I have tried without the -ignh option, but N- and C-terminal atoms coming
from the .tdb file are not recognized by pdb2gmx. I have tried with the
-ignh option but that modified my coordinates...

Any suggestion will be welcome!


[ Nicolas Sapay Ph.D. ]
University of Calgary, Dept. of Biological Sciences
2500 University Dr. NW, Calgary AB, T2N 1N4, Canada
Tel: (403) 220-6869
Fax: (403) 289-9311

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