[gmx-users] deprotonated HIS in AMBER03 force field

[Justin A. Lemkul]

Yuno Lee wrote:
> Hi all,
> 
> I'm simulating with zinc finger protein NMR structure (PDB ID: 2JUN).
> 
> In this protein, only deprotonated HIS and CYS are placed with zinc ions.
> 
> So, we tried with AMBER03 force field which has deprotonated CYS as CYM. 
> 
> But I couldn't find about deprotonated HIS in ffamber03.rtp file.
> 
> 
> Could anyone plz tell me how to use deprotonated HIS?
> 

If that particular residue is not part of the original force field, you have to 
do one of the following:

1. Find suitable parameters in the literature
2. Derive the parameters if they do not exist

If you are unfortunate and #2 is the case, you will have to go through the 
time-consuming and difficult process of parameterization.  See here:

http://oldwiki.gromacs.org/index.php/Parameterization

And especially:

http://oldwiki.gromacs.org/index.php/Exotic_Species

-Justin

> 
> Thank you all
> 
> -- 
> Thanks & Regards,
> 
> 
> Yuno Lee, Master of Science
> 
> ---------------------------------------
> Technical Research Personnel
> Computational Biology & Bioinformatics Lab (CBBL)
> Environmental Biotechnology National Core Research Center (EB-NCRC)
> Department of Biochemistry and Division of Applied Life Science (BK21 
> program),
> Gyeongsang National University (GNU)
> 900 Gazwa-dong, Jinju, 660-701 Korea
> Email: yuno at gnu.ac.kr <mailto:yuno at gnu.ac.kr>, youknow at bio.gnu.ac.kr 
> <mailto:youknow at bio.gnu.ac.kr>
> Homepage: http://bio.gnu.ac.kr/~youknow
> ---------------------------------------
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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