On 2012-04-05 06:19:07AM -0700, Acoot Brett wrote: > Dear All, > > For pdb2gmx, we have -ignh. Does -ignh will always give the correct HIS > format at pH 7?
-ignh does not do what you think it does. -ignh ignores the original PDB's hydrogen coordinates. Picking the "correct" histidine protonation at pH 7 is still structure- dependent since either nitrogen can be protonated. The manual for pdb2gmx states the following automatic HIS protonation: "For His, this is based on an optimal hydrogen bonding conformation. Hydrogen bonds are defined based on a simple geometric criterium, specified by the maximum hydrogen-donor-acceptor angle and donor-acceptor distance, which are set by -angle and -dist respectively." -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
