On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett <acootbr...@yahoo.com> wrote: > Dear All, > > For the different protonation state of HIS, what are there 3-letter code for > GROMACS? And how about -SH and -S-S- codon? Or do you have a web link for me > to read? Do we still have any other confusing amino acids?
In pdb2gmx -his you will get something like below 0. H on ND1 only (HSD) 1. H on NE2 only (HSE) 2. H on ND1 and NE2 (HSP) 3. Coupled to Heme (HIS1) Then based on the pka value and the PH, you can make a choice. > > I am looking forward to getting a reply from you. > > Cheers, > > Acoot > > -- > 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 -- 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
