AMBER: charges in PBSA calculation

From: Neha Gandhi <>
Date: Sun, 19 Aug 2007 10:20:16 +0800


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.

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

Kindly advice.
Curtin university of technology

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Received on Sun Aug 19 2007 - 06:07:59 PDT
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