Hi allI 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
siteI 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 choose0. 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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