[gmx-users] the different protonation state of HIS

[lina]

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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