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: [email protected] <mailto:[email protected]>, [email protected]
<mailto:[email protected]>
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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