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 Tue Sep 10 2013 - 23:00:03 PDT
