AMBER Archive (2009)

Subject: Re: [AMBER] apbs-amber

From: Rilei Yu (
Date: Tue Sep 22 2009 - 20:41:08 CDT

Dear Robert,

Thanks for your kind remind, that may be the problem. So if I make a box that is big enough, it will spend me more time to calculate, is not it? But I will have a try immediately!

Best wishes,

Rilei Yu

--- 09年9月23日,周三, Robert Konecny <> 写道:

发件人: Robert Konecny <>
主题: Re: [AMBER] apbs-amber
收件人: "AMBER Mailing List" <>
日期: 2009年9月23日,周三,上午7:18


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
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