AMBER Archive (2007)

Subject: AMBER: charges in PBSA calculation

From: Neha Gandhi (n.gandhiau_at_gmail.com)
Date: Sat Aug 18 2007 - 21:20:16 CDT


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

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