Hello!
> what I have to do with
> amynocayl-trna? The PO3 end of adenyne must be connected to the next
> nucleotide, (one free valence of P) I have to leave this place empty or I
> have to add H there?
Accurate parametrization of a molecular fragment is an advanced task.
You can find instructions at
http://q4md-forcefieldtools.org/Tutorial/
(Tutorial I - III)
and at
http://ambermd.org/tutorials/advanced/tutorial1/
--
Dmitry Nilov
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
web: http://enzyme.fbb.msu.ru/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 26 2011 - 12:30:03 PDT
