AMBER Archive (2007)

Subject: Re: AMBER: charges in PBSA calculation

From: Ray Luo (rluo_at_uci.edu)
Date: Sun Aug 19 2007 - 08:32:19 CDT

Are you using Amber8? Have you patched all bugfixes for it?

Best,
Ray

On Aug 18, 2007, at 10:20 PM, Neha Gandhi wrote:

> 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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