<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 > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > >
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 -- [ 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
