[gmx-users] the different protonation state of HIS

[Justin A. Lemkul]

Acoot Brett wrote:
> Dear All,
>  
> For pdb2gmx, we have -ignh. Does -ignh will always give the correct HIS 
> format at pH 7?
>  

Strictly speaking, the -ignh option doesn't have anything to do with HIS 
protonation, it simply ignores H atoms in the input.  HIS protonation states are 
then determined by an algorithm that seeks to maximize the hydrogen bonding 
network in the structure.  Whether or not that necessarily reproduces reality 
(or completely replicates any protonation states in the original input that had 
its H atoms ignored) is an exercise for the user and can be changed with -his.

-Justin

> Looking forward to getting your reply.
>  
> Cheers,
>  
> Acoot
> 
> *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 
> <mailto: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
>  >
>  > --
>  > gmx-users mailing list    gmx-users at gromacs.org 
> <mailto:gmx-users at 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-request at gromacs.org 
> <mailto:gmx-users-request at gromacs.org>.
>  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================