[gmx-users] the different protonation state of HIS
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 5 15:22:40 CEST 2012
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.
> 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
> <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
> > --
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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