AMBER Archive (2009)

Subject: Re: [AMBER] probelm-APBS

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Sun Oct 04 2009 - 19:51:10 CDT

Thanks for your help! Based on your suggestion, I may send the request to the APBS forum.

Regards,
Rilei Yu

--- 09年10月5日，周一, Robert Konecny <rok_at_ucsd.edu> 写道：

发件人: Robert Konecny <rok_at_ucsd.edu>
主题: Re: [AMBER] probelm-APBS
收件人: "AMBER Mailing List" <amber_at_ambermd.org>
日期: 2009年10月5日,周一,上午8:20

Hi,

are you using the Amber MMPBSA scripts? It is not obvious from your email.

I don't really understand what you are trying to do here. It does not make
sense to center the coarse grid on one molecule and the fine grid on
another - the result will be wrong.

The APBS users mailing list might be more appropriate forum to help you get
going with APBS calculations.

Best,

Robert

On Sat, Oct 03, 2009 at 01:41:07PM +0800, Rilei Yu wrote:
> Dear anyone who may concern this letter,
>
> When I was using apbs to calculate the eletrostatic binding Energy, I found when:
>    dime  240 240 240
>        cglen 120 120 120
>        fglen 90 90 90
>        cgcent mol 1
>        fgcent mol 1
> That would be ok, but when I used the script:
> dime  240 240 240
>
>        cglen 120 120 120
>
>        fglen 90 90 90
>
>        cgcent mol 1
>
>        fgcent mol 3,
> there is following errors:
> NOsh_setupCalcMGAUTO:  Error!  Finest mesh has fallen off the coarser meshes!
> NOsh_setupCalcMGAUTO:  difference in min 1-direction = 0.3355
> NOsh_setupCalcMGAUTO:  min fine = 32.546 -10.8485 6.95322e-310
> NOsh_setupCalcMGAUTO:  min coarse = 6.44 -10.513 6.95314e-310
> VASSERT: ASSERTION FAILURE!  filename nosh.c, line 1581, (0)
> Aborted
> I want to make the center of my grid as the cernter of the complex (mol1), then on the center of the ligand (mol3). I ever used this approach to calculate some other similar complex, to to this complex it does not work!
>
> Can anyone give me some suggestions?
>
> Rilei Yu
>
>
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