Sorry for late reply and million thanks!
best,
Jin Yang
On Tue, Nov 8, 2011 at 5:43 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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 Thu Nov 10 2011 - 08:00:03 PST
