You should choose satlcon/istrng based on the conditions you want to
simulate. Also, molsurf is not implemented in the python version of MM-PBSA
yet. I can't comment on the physical meaning of CUTCAP. I will leave that
for a PB developer, or someone else more knowledgeable.
-Bill
On Wed, Nov 23, 2011 at 7:45 AM, Qinghua Liao <fantasticqhl.gmail.com>wrote:
> Dear amber users,
>
> I have some problems on the parameters in mm/pbsa calculations.
>
>
> 1. The default values of istrng and saltcon are 0.0, but in the python's
> tutorial, both of them are set as 0.10, and also sometimes 0.15. So how
> should I choose them according to my own system?
>
> 2. CUTCAP is set to -1.0, does that mean that the radius of the water
> sphere is big enough to enclose the whole solute?
>
> 3. What's the default method for nonpolar solvation energy in python's
> version? How should I do If I want to set MS==1, just place MS=1 in the
> general list?
>
> Thanks very much for any response.
>
> --
> Best Regards,
>
> Qinghua
> Ph.D. student
> Juelich Research Center
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 23 2011 - 05:00:04 PST
