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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 28 08:02:29 CET 2007

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...


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