AMBER Archive (2007)

Subject: AMBER: Heme and CYS !!

From: Pradipta Bandyopadhyay (pradipta_b_at_mail.jnu.ac.in)
Date: Fri Oct 26 2007 - 05:49:47 CDT

Dear all,

 My protein has a heme, whose one Carbon atom is bonded to S of Cysteine. I am taking the HEME parameters as given in the AMBER contributed parameter set. However, for forming bond between the S of Cysteine and Carbon of HEME, I am not sure
which CYS unit to take - CYS or CYM (CYX is for S-S linkage, so I don't think I should use this).

I don't want to form any new unit of cysteine. Can I do it with any exisiting unit of Cysteine? Has anybody done this?

thanks,

  Pradipta

Dr. Pradipta Bandyopadhyay
Centre for Computational Biologya and Bioinformatics
School of Information Technology
Jawaharlal Nehru University, New Delhi, INDIA
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