AMBER Archive (2009)

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

From: Jason Swails (jason.swails_at_gmail.com)
Date: Tue Nov 24 2009 - 23:33:31 CST

Rilei,

Robert may correct me if I'm wrong here, but I'll answer what I believe is
correct. For the values, make sure you're using the correct units. Amber
uses the units kcal/mol whereas APBS uses kJ/mol (so if you're off simply by
a factor of 4.184, that is probably why). Furthermore, when you use APBS
standalone, are you positive that you're using the same set of charges (i.e.
the partial charges located in the Amber topology file). These two issues
could easily throw your numbers way off.

To solve the 'grid-box', upgrade to the new iapbs version that was just
recently released. That issue is solved there.

Good luck!
Jason

2009/11/25 Rilei Yu <yulaomao1983_at_yahoo.com.cn>

> 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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-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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