Dear Jin Yang,
> 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?
This can be generated by using R.E.D. Server...
You follow: http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#18
for a Cytidine (nucleoside) with a CH2SH group . C6: -1- (2 molecules)
You follow: http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
for a S-methylated cysteine dipeptide -2- (1 molecule)
You need an additional inter-molecular charge constraint between the
SH group of -1- and the methyl group of -2-.
So you need 3 molecules:
- two intra-molecular charge constraints (INTRA-MCC) to define the
central fragment of your modified Cysteine
- an inter-molacular charge constraint (INTER-MCC) between the
modified cysteine dipeptide (methyl group) and the modified Cytidine
(thiol group)
- two inter-molacular charge constraints between the modified Cytidine
and dimethylphopshate
R.E.D. will generate three fragments: phosphate + pseudo Cytidine +
pseudo Cysteine; then, you will have to adapt the residue & atom names
in your PDB file according to these in the FF libraries generated by
R.E.D.; brain storming/interesting, but it should work ;-)
regards, Francois
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Received on Tue Nov 08 2011 - 03:00:03 PST
