AMBER Archive (2009)

Subject: Re: [AMBER] i-APBS and apbs

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Wed Nov 25 2009 - 05:14:15 CST

Dear Dr. Robert and Jason,

Thanks for your reply! Here, I cannot say too much, may be I made some mistake. But the mainly problem is that I really want to use i-APBS in the "mmpbs.in" from the new script. In the new script, how can I explicitly set up the gid-box?

When I used APBS, the final values is -9.259764699222E+00 kJ/mol, while when I used the new script the values is - 0.5 kal/mol (indi=4, exdi=78.5) and 68kal/mol (all parameters are default) respectively! When I used apbs, the values, are usually influenced by the dimension of the grid-box and the internal dielectric.  So, here I assumed the values calculated in the scipt may not be converged unless the grid-box is big enough. As a user, I admit my assumption is crude. 

I have attached all my file to this email.

Rilei Yu

--- 09年11月25日，周三, Robert Konecny <rok_at_ucsd.edu> 写道：

发件人: Robert Konecny <rok_at_ucsd.edu>
主题: Re: [AMBER] i-APBS and apbs
收件人: "AMBER Mailing List" <amber_at_ambermd.org>
日期: 2009年11月25日,周三,下午1:33

Hi Rilei,

the results of APBS and sander.APBS (electrostatic or solvation energies
and forces) should be exactly the same as long as you are using the same
input parameters. What atomic charges and radii are you using for your
sander.APBS and APBS calculations?

You can explicitly set grid size using cglen and fglen parameters while
calc_type is set to 1. See
http://mccammon.ucsd.edu/iapbs/usersguide/using-amber.html for more
details.

Good luck,

Robert

On Wed, Nov 25, 2009 at 01:14:18PM +0800, Rilei Yu wrote:
> Dear amber users,
>
> The values calculated using APBS and i-APBS is always very different,
> even though I set up very similar parameters. What is more, when i use
> i-APBS, there are some complains that indicate the grid-box is a bit of
> small. Is there any way to set up the dimension of the grid box in iAPBS?
>
> Thanks for your help!
> Best Regards,
>
> Rilei Yu
>
>
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