AMBER: charges in PBSA calculation

From: Neha Gandhi <n.gandhiau.gmail.com>
Date: Sun, 19 Aug 2007 10:20:16 +0800

Hi,

I have been performing pbsa calculations for charge ligands like
glycosaminoglycans. But I the PBTOTAL is high negative (-1000 Kcal/mol)
which is not accurate. I used the internal pbsa electrostatic potential
calculator in amber 9 rather than external programs like delphi. Is it
possible that internal pbsa will not work for charged ligands according to
this tutorial.
http://www.teokem.lu.se/~ulf/Methods/mm_pbsa.html

Do I need external program or there is something wrong with my calculations?

Kindly advice.
Cheers,
Neha
Curtin university of technology

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Aug 19 2007 - 06:07:59 PDT
Custom Search