Dear Gustavo,
> I need to parametrize a ligand that is a tripeptide blocked with
> terminal groups that are not available in the Amber parameter
> database:
>
> Boc-Gly-Arg-Arg-AMC (see:
> http://www.chemexper.com/chemicals/supplier/cas/113866-14-1.html)
>
> Where:
> Boc = t-butiloxy-carbonyl
> AMC = 7-amine-4-methyl-coumarin
>
> Could someone suggest what would be the best way to do it? I
> considered just using antechamber for it, but since the amino acids
> are available in the regular force fields, I imagine it could be best
> to just use those parameters for the amino acids. Is that correct? If
> this is the case, what would be the best procedure to parametrize the
> terminal groups? What should I do to ensure a good description of the
> bonds/angles involving both terminal group and amino acid atoms?
Your two chemical groups are new capping groups: you could define
intra-molecular charge constraints (INTRA-MCC keyword in a P2N file)
set to zero in the two corresponding P2N files for the NHMe or COMe
capping groups.
You could test the following models:
tert-butyloxycarbonyl-NHMe
7-amine-4-methyl-coumarin-COMe
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
If you decide to use R.E.D. Server, the statistics module of R.E.D. IV
will directly report the differences between the charge values
generated without and with the intra-molecular charge constraint for
each molecule.
I hope this helps.
regards, Francois
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 20 2011 - 01:00:03 PDT
