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

From: Thakur, Abhishek <axt651.miami.edu>
Date: Mon, 1 Aug 2016 18:42:29 +0000

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 - 12:00:02 PDT
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