On Tue, Mar 09, 2004, opitz.che.udel.edu wrote:
>
> When I define my own residues in leap, I have to define the atom type
> (e.g. h1, c3, hn, etc.). Do I also have to define the charge of the
> individual atoms? If so, where do I find the information on this to do it?
Charges for amber are generally determined by a RESP procedure. There
is a link on the Amber web page to help for this. You can also use the
AM1-BCC procedure; see the Antechamber chapter of the Users' Manual.
>
> On a different note, what is the difference between the nucleotides
> defined in the different libraries (e.g. DAN vs. DA)?
Please see p. 40 of the Amber 7 Users' Manual.
....good luck...dac
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Mar 10 2004 - 16:53:00 PST
