Hi AT,
On Fri, Jul 15, 2016 at 9:16 AM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi
>
> I was going through manual for
>
>
> istrng=0.100, prbrad=1.4, radiopt=0, inp=2,
> indi=1.0, exdi=80.0, sander_apbs=0, scale=2.0,
> cavity_surften=0.0378, cavity_offset=-0.5692
> /
>
>
> found that all the things set up are default parameters.
>
> So If things are default then do I need to write it on my script?
No you don't have to set default values.
>
>
> So If I use this script
>
>
> istrng=0.100,
> inp=2, radiopt=0
> /
>
> It should be same? Because in upper script everything is set as default value? It should take it automatically if I don't mention it in my script right?
>
>
> I was also seeing that cavity_surften=0.0378 only works in inp=1.
>
>
> Now I am confused I should go with inp=1 or 2.
>
> If anyone can explain me
>
> inp = Non polar optimization method (Default=2)
>
> Which gives better result?
>
> As I was seeing that non polar model for PB is more destablized than simple model.
>
> Does it mean if I use inp = 1 then it will use simple model?
>
See my previous reply regarding INP=1 or 2.
All the best,
Ray
--
Ray Luo, Ph.D.
Professor
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
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Received on Fri Jul 15 2016 - 14:00:02 PDT
