[gmx-users] Cytochrom C

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 10 22:29:35 CET 2012

Dariush Mohammadyani wrote:
> Dear Justin,
> I could not find HIS in CHARMM and GROMOS53a6. Somebodies offer to 
> rename it to HSE or HSD, but I do not know why? and which one is 
> correct. I am working on Cytochorom c.

They refer to different protonation states, either epsilon or delta.  The name 
in the .pdb file will be HIS (per standard nomenclature), but pdb2gmx will 
choose the protonation state it thinks is appropriate based on hydrogen bonding 
networks.  You can manually set protonation state with the -his flag.  For 53A6, 
HISA is delta protonation and HISB is epsilon.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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