AMBER Archive (2007)

Subject: AMBER: generating topology files for PBSA

From: saccenti_at_cerm.unifi.it
Date: Fri Oct 05 2007 - 04:46:14 CDT

Hi Amber Folk,

I have the topology file for a complex (A + B) that I minimized in water
(adding ions to equilibrate charge)
On this complex I run a MD in water and I get the trajectory files.

To run PBSA I need topology files for A and B separately.

But in which way generate topology for A and B?

Just the two protein, or adding water and ions to euilibrate charges of A
and B?

I think the number of water added to A and B separately will be not the same
of water added to A+B.

It will be an issue?

many thanks
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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