[gmx-users] the different protonation state of HIS

lina 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.
> Cheers,
> Acoot
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