AMBER Archive (2007)

Subject: Re: AMBER: charges in PBSA calculation

From: Neha Gandhi (n.gandhiau_at_gmail.com)
Date: Sun Aug 19 2007 - 18:01:47 CDT

Hi,
I am using Amber 9. Do I need to add ions to the charged ligand file? But in
that case, the number of atoms in the complex and the ligand will not match
and the pbsa calculation will stop. How do I perform pbsa calculations for
charges ligands?

Your help is appreciated.
Regards,
Neha

On 8/19/07, Ray Luo <rluo_at_uci.edu> wrote:
>
> 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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