Dear All, I need your advices about how to define a modified cytosine(C6)
which is covalently bonded to the sulfer of cysteine residue. In my case,
the cytosine is methylated and form a covalent bond with nearby cysteine
simultaneously. I try to define a new cytosine manually in which I would
like to treat the methyl group and bonded cysteine as two adducts on the
base. However, the bonded cysteine is part of the backbone of the enzyme
(methyltransferases) and the cytosine is part of the DNA strand. So I can't
cut the cysteine off from its chain and add it into part of the cytosine.
My question is how can I indicate this cysteine is covalently bonded to the
cytosine in the pdb file and it can be recognized when I load it in AMBER?
Any suggestions?
Thanks very much!
sincerely,
Jin Yang
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Received on Mon Nov 07 2011 - 11:30:03 PST
