Dear Dr. Ray,
Thank you very much for your rapid reply.
To use Tan & Luo radii, by setting radiopt=1 and inp=2,
appropriate values are set to the others automatically, aren't they?
I'll try.
Thanks,
WATANABE
> WATANABE,
>
> For PB, please only set radiopt=1 and inp=2. If you don't feel
> comfortable with setting the many options, don't set other options
> such as ARCRES, SURFTEN, SURFOFF since the default values has been set
> to be compatible in the program.
>
> Also, the python script is somewhat more robust in setting options if
> you really want to try these options out ...
>
> Ray
>
> On Wed, Sep 11, 2013 at 1:56 AM, Hiromasa WATANABE
> <hi-watanabe.hpc.co.jp> wrote:
>> Dear Amber supporters,
>>
>> I'm trying MM/PBSA calculation and MM/GBSA calculation using AMBER12's MM_PBSA.
>> In order to perform same calculation as Lei Xu et al., J. Phys. Chem. B 117, 8408 (2013),
>> I've created input file like below.
>> Would you please check if parameter values and consistency are OK?
>>
>> (1)
>> In MM/PBSA calculation, to use Tan & Luo radii,
>> according to the AMBER manual(p.329),
>> values of SURFTEN and SURFOFF are set like below, is this OK?
>>
>> .GENERAL
>> MM 1
>> GB 0
>> PB 1
>> MS 1
>>
>> .MM
>> DIELC 1.0
>>
>> .PB
>> PROC 2
>> REFE 0
>> INDI 1.0
>> EXDI 80.0
>> SCALE 2
>> LINIT 1000
>> ISTRNG 0.0
>> RADIOPT 1
>> ARCRES 0.0625
>> INP 2
>>
>> SURFTEN 0.005
>> SURFOFF 0.86
>>
>> IVCAP 0
>> CUTCAP -1.0
>> XCAP 0.0
>> YCAP 0.0
>> ZCAP 0.0
>>
>> .MS
>> PROBE 0.0
>>
>> (2)
>> In MM/GBSA calculation, to use Onufriev's GB and LCPO method,
>> following settings are OK?
>>
>> .GENERAL
>> MM 1
>> GB 1
>> PB 0
>> MS 1
>>
>> .MM
>> DIELC 1.0
>>
>> .GB
>> IGB 2
>> GBSA 1
>> SALTCON 0.00
>> EXTDIEL 80.0
>> INTDIEL 1.0
>>
>> SURFTEN 0.005
>> SURFOFF 0.00
>>
>> .MS
>> PROBE 0.0
>>
>>
>> Best regards,
>> WATANABE
>>
>> --
>> 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 8789 (20130911) __________
>
> The message was checked by ESET NOD32 Antivirus.
>
> http://www.eset.com
>
>
>
>
--
ＨＰＣシステムズ株式会社 （ http://www.hpc.co.jp/ ）
HPC事業部 技術グループ 渡邊 啓正 <hi-watanabe.hpc.co.jp>
〒108-0022 東京都港区海岸3-9-15 LOOP-X 8階
TEL：03-5446-5530（代表）／FAX：03-5446-5550（共通）
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 Wed Sep 11 2013 - 18:30:02 PDT
