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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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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