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.lastn...@gmail.com>
*To:* Acoot Brett <acootbr...@yahoo.com>; Discussion list for GROMACS
users <gmx-users@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 <acootbr...@yahoo.com
<mailto:acootbr...@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
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
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