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

Nicolas SAPAY nsapay at ucalgary.ca
Wed Feb 28 18:01:05 CET 2007

<quote who="Mark Abraham">
> 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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Most of the time the difference is not significative. But sometimes, the
addition of hydrogens by pdb2gmx lead to atom clashes. The problem comes
from the rules defined in my hdb file and the CHARMM nomenclature. Two
hydrogens bonded to a same carbon can be named H#X and H#Y (# = carbon
number). This is not convenient for the hdb format which prefers hydrogen
names like HX# or HY#. Actually, I have defined H#X and H#Y using 2 hdb
entry with rule 6. So I use two times the rule 6 on the same carbon
instead of one... This is not very elegant but I don't want to modified
the CHARMM atom nomenclature. Maybe should I play more with hydrogens
addition rules of the hdb file to obtain something correct ?

[ 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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