Quoting prateeksha s <prateeksha.s.gmail.com>:
> I want to simulate protonated adenine. So which charge scheme one should use
> for that?
You need to generate your own library to the Tripos or OFF (or prep)
format for your molecule. I guess you even need to generate a new
library for a molecule fragment (compatible with fragments already
available) and not for the molecule itself.
To generate a new molecule fragment see first the following article:
Cieplak et al. J. Comput. Chem., 1995, 16, 1357-1377
Then, you can generate the fragment you are interested in following a
strategy described .
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#14
See "Scheme 4" in particular.
You will find examples of new nucleic acid fragments in R.E.DD.B. .
http://q4md-forcefieldtools.org/REDDB/up/F-59/
or
http://q4md-forcefieldtools.org/REDDB/up/F-58/
> Also, I'm having troubles with xleap displaying the protonated adenine. The
> un-protonated adenine displays fine. But, the Hs in protonated adenine are
> not getting recognized.
This is normal because your molecule is not recognized by LEaP. You
need to create your own library.
regards, Francois
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Apr 18 2008 - 21:12:48 PDT
