AMBER Archive (2009)

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

From: Robert Konecny (rok_at_ucsd.edu)
Date: Tue Nov 24 2009 - 23:33:37 CST

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
>
>
> ___________________________________________________________
> 好玩贺卡等你发，邮箱贺卡全新上线！
> http://card.mail.cn.yahoo.com/
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber