On 2012-04-05 08:55:24PM +0800, lina wrote: > 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
This is also somewhat forcefield dependent (and how you name the histidines in the PDB as well). > > 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? -SH will show up as part of a -SH containing residue (cysteine). pdb2gmx will attempt to ask you about -S-S- bridges correctly if two cysteines are close to each other, use the -ss parameter to pdb2gmx. The manual has a description of how to force a disulfide bridge using specbond.dat if the starting structure is suboptimal... -- 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
