AMBER Archive (2009)
Subject: Re: [AMBER] apbs-amber
From: Robert Konecny (rok_at_ucsd.edu)
Date: Tue Sep 22 2009 - 18:18:28 CDT
if your apbs calculated binding energy significantly changes with the grid
size that suggests that your grid is not sufficiently large. In the apbs
input you provided below your grid spacing is 1A which is way too coarse
for electrostatic energy calculation. You will need to increase your grid
so the spacing is less than 0.5A.
On Tue, Sep 22, 2009 at 03:58:40PM -0700, Rilei Yu wrote:
> Hi amber users,
> When I used apbs to calculate the binding energy between my protein and its ligand, I found the energy value change greatly with the value of the Grid box. So, now I thinks there may be some problem on my calculation. So I want to know, how amber do this job(to adjust the grid-box for different kind of complex with different size)?
> ( dime 65 97 129
> cglen 97.5 145.5 193.5
> fglen 65 97 129
> cgcent mol 1
> fgcent mol 3)
> Thanks for your help in advance?
> Rilei Yu
> AMBER mailing list
AMBER mailing list