Ok, thank you, but i don't understand if I have to minimize (optimize)
ligand structure and in what params before antechamber usage, or not?
whether a ligand conformation will have an effect on prmtop content or not?
Thank you again
2011/9/26 Dmitry Nilov <nilovdm.gmail.com>
> 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/
>
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>
--
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Received on Mon Oct 03 2011 - 14:30:04 PDT
