Nicolas SAPAY wrote:
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...
Small coordinate changes in hydrogen coordinates are not going to
matter. If CHARMM generated them, they're probably just using slightly
different heuristics. The differences here will be dwarfed by the
perturbations in the equilibration process...
Mark
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