Dear Dr. Ray,
Thank you very much for your rapid reply!
I understood. I look forward to the patch.
Thanks,
WATANABE
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> __________ Information from ESET NOD32 Antivirus, version of virus signature database 8883 (20131006) __________
>
> The message was checked by ESET NOD32 Antivirus.
>
> http://www.eset.com
>
>
>
>
--
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 08 2013 - 23:30:03 PDT
