AMBER Archive (2007)

Subject: Re: AMBER: MM_PBSA with complex plus Ion

From: Pankaj Daga (pdaga_at_olemiss.edu)
Date: Sun Sep 23 2007 - 10:50:21 CDT

Hey Edo,

I guess, while mentioning about receptor in binding energy
script, following modifications should be done.

NUMBER_REC_GROUPS 2
RSTART 1
RSTOP end of rec atom number
RSTART METAL ION NUMBER
RSTOP LAST NUMBER OF METAL ION

Seniour members in the group can suggest if this
modification is wrong.

Hope this will help.

Cheers

Pankaj

> I have a question about how to treat a complex with a
> metal ion. That is a I have a complex of the form
> A-i-B where A and B are protein and i a metal ion that is
> bonded to both A and B.
> I would like to extimate the stability and binding energy
> following the tutorial exemples that is indeed very clear.
>
> As I need prm top files for Ligand and receptor how to
> treat the ion?
>
> Many thnks for any clue!
>
> Edo
>
>
> --
> Dr Edoardo Saccenti
> CERM Magnetic Resonance Center
> University of Florence
> Fiorgen Foundation
> Via Luigi Sacconi n° 6
> 50019 Sesto Fiorentino
> (FI) Italy
> Tel: +39 055 4574281
>
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