AMBER Archive (2006)

Subject: Re: AMBER: SURFTEN in GB (mm_pbsa calculations)

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Aug 03 2006 - 14:38:59 CDT

Your simulation involves some pretty advanced techniques- not only
do you need to know how the nonpolar solvation energy scales with
buried surface area in acetone, but you also need to worry about the
exernal dielectric and whether this GB model is even appropriate for
non-aqueous solvents. Unless you are very familiar with these topics
or are following published work that provides these values then I would
suggest not using GBSA as a solvent model for acetone.

Shuting Wei wrote:

> Hello, all
>
> I am tring to calculate the GB energy with mm_pbsa for a system with
> acetone as solvent. As i know, the SURFTEN = 0.0072 is used for system
> with water as solvent. How can i find out the correct value for
> SURFTEN for system containing acetone solvent? Also, for the
> calculation for SASA, is the value of SASA correct if i use LCPO or
> molsurf method for the calculation of acetone system?
>
> Thank you in advance,
>
> Shuting Wei
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu