Dear WATANABE,
*
*
I think you may directly ask the authors for an original input file£¿
Best regards,
Baifan Wang
2013/9/11 Hiromasa WATANABE <hi-watanabe.hpc.co.jp>
> 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
>
--
Baifan Wang, Ph.D.
State Key Laboratory of Elemento-Organic Chemistry
Department of Chemical Biology College of Chemistry
Nankai University
TIANJIN, 300071, P. R. CHINA
E-mail: ferlich.comput.gmail.com
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Received on Wed Sep 11 2013 - 00:30:03 PDT
