I already replied to this exact question (verbatim):
http://www.gromacs.org/pipermail/gmx-users/2008-July/035300.html
What have you done to help yourself solve this problem? Posting repeat
questions that do not address any of the comments you receive will lead to your
posts likely getting ignored. When asking for free help, make it obvious that
you are willing to take advice and help yourself.
-Justin
najwa drici wrote:
Hi all
I work with a protein where 3 CYS redisidues make bond with a Zn atom by its SG
atoms and HIS redisidue makes bond with a Zn atom by its NE2 in active site
I want to use deprotonated “cys”. In manual for “pdb2gmx “ clearly says on
option of choosing Cys protonated state possibility but why that option not
appearing while running “pdb2gmx” , just like for “Arg”, “His”, “Asp” and “Glu”.
Must i generate a specbond.dat entry for Cys-Zn His-Zn linkage ?
And what type of histidine do I have to choose
0. H on ND1 only (HISA)
1. H on NE2 only (HISB)
2. H on ND1 and NE2 (HISH)
3. Coupled to Heme (HIS1)
Best regards
Nedjoua Drici
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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