Hi, Yongchun
MM-PBSA don't use the explicit solvent. The solvation effect is simulated
with the continuum solvation model. You may need to remove your explicit
solvent and counter ions when performing MM-PBSA calculations!
If you've already removed explicit solvents and just want the MM energy be
calculated with periodic boundary conditions, I think this doesn't make
sense and is incorrect.
Regards!
Liu
On Wed, 05 Apr 2006 03:47:06 -0300, 杜永春 <duyongchun.mail.nankai.edu.cn>
wrote:
> hi,Amber
> I use mm_pbsa programe to compute binding energy.There is a periodic
> boundary
> in my prmtop file .But when running ,it creates a sander_com.in file.In
> this file
> ,the NTB=0,whith means that no periodicity is applied.How can I modify
> the
> mm_pbsa.in file and then I can change the NTB?Thanks!
> Yongchun Du
> 2006.4.5
>
>
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--
JunJun Liu
College of Chemistry
Central China Normal University
WuHan 430079
P.R. China
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Received on Fri Apr 07 2006 - 17:17:59 PDT
