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
>
> _______________________________________________
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Received on Wed Sep 11 2013 - 06:30:02 PDT
