Re: [AMBER] default value (inp= 0,1,2)? MMPBSA

From: Ray Luo <rluo.uci.edu>
Date: Mon, 1 Aug 2016 12:25:42 -0700

AT,

I think the default is INP=1 in the python script ... it's INP=2 in
the fortran code, i.e. sander/pbsa ...

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
On Mon, Aug 1, 2016 at 11:42 AM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi
>
> I have a question that if I don't mention 0,1 or 2 then by default amber will consider which model?
>
>
> Thanking you,
>
> AT
>
> ________________________________
> From: Ray Luo <rluo.uci.edu>
> Sent: Monday, August 1, 2016 6:35:04 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] default value (inp= 0,1,2)? MMPBSA
>
> AT,
>
> INP=0 turns off nonpolar solvation model; INP=1 is the classical model
> that uses a single surface tension to correlate with the nonpolar
> solvation free energy; and INP=2 is the modern model that uses two
> terms to correlate with dispersion and hydrophobic terms separately.
> See
>
> Tan, et al, The Journal of Physical Chemistry B 111 (42), 12263-12274, 2007
>
> 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
>
>
> On Mon, Aug 1, 2016 at 9:35 AM, Thakur, Abhishek <axt651.miami.edu> wrote:
>> Hi
>>
>> I am doing MMPBSA calculation,
>>
>> I would like to know for inp = 0,1,2 what is the default value in amber.
>>
>> As I can understand all are 3 different model, but curious to know what is the default model.
>>
>>
>>
>> Thanking you,
>>
>> AT
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Received on Mon Aug 01 2016 - 12:30:04 PDT