Re: [AMBER] About INP in case of MS=1

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Thu, 3 Oct 2013 10:00:53 -0700

Hiromasa,

Yes, that's because the PB radius definition gets changed when INP=1
or when INP is the default value of 2.

Wes will upload a patch to Amber12 to force the default radius
definition (radiopt) to remain as 0 whether INP=1 or INP=2. This has
been the case in the latest AmberTools release.

Ray

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Wed, Oct 2, 2013 at 10:55 PM, Hiromasa WATANABE
<hi-watanabe.hpc.co.jp> wrote:
> Hi,
>
> About MM_PBSA in AMBER12, according to the manual,
> INP is a option for the case of MS=0, and INP has no influence in case of MS=1, I think.
>
> But, when MS=1,
> (1) INP=1
> (2) #INP=1
> these two computation produce different PBCAL.
>
> Does INP influence PB calculation in case of MS=1 ?
>
> How should I set INP when MS=1 ?
>
> --
> Hiromasa WATANABE
> Manager, Ph.D.
> HPC Dept., Technology Gr., HPC SYSTEMS Inc.
> Head office: LOOP-X 8F, 3-9-15 Wangan, Minato-ku, Tokyo, Japan 108-0022.
> Email: hi-watanabe.hpc.co.jp
> www.hpc.co.jp
>
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Received on Thu Oct 03 2013 - 10:30:12 PDT