[gmx-users] the different protonation state of HIS

Acoot Brett acootbrett at yahoo.com
Thu Apr 5 15:19:07 CEST 2012

Dear All,
For pdb2gmx, we have -ignh. Does -ignh will always give the correct HIS format at pH 7?
Looking forward to getting your reply.

 From: lina <lina.lastname at gmail.com>
To: Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Thursday, 5 April 2012 10:55 PM
Subject: Re: [gmx-users] the different protonation state of HIS
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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