[gmx-users] the different protonation state of HIS
lina.lastname at gmail.com
Thu Apr 5 14:55:24 CEST 2012
On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett <acootbrett at 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.
> gmx-users mailing list gmx-users at gromacs.org
> 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users