Dear Dr. Ray,
To do same calculation as the paper J. Phys. Chem. B 117, 8408 (2013),
in my thoughts, its values seems to be different from the default ones of MM_PBSA program.
Here's a summary of information of the paper:
In both MM/GBSA and MM/PBSA:
* SASA based on LCPO algorithm is used for nonpolar desolvation free energy (dG_SA).
dG_SA = 0.0072 x dSASA
* Interior dielectric constant (solute) is 1, 2 or 4.
Exterior dielectric constant (solvent) is 80.
In MM/GBSA:
* Onufrievs' modified GB is used for polar desolvation free energy (dG_GB).
In MM/PBSA:
* Tan & Luo radii is used for polar desolvation free energy (dG_PB).
Therefore, I set,
INDI=1.0, EXDI=80.0 in both MM/GBSA and MM/PBSA.
IGB=2 in MM/GBSA.
RADIOPT=1, INP=2 in MM/PBSA.
Q1.
According to the explanation of "MS" in AMBER manual,
to use LCPO, MS=0 and GB=1 for MM/GBSA,
but I don't know that for MM/PBSA.
Does MS=0 and PB=1 work fine?
Q2.
In the above paper, dG_SA = 0.0072 x dSASA.
So, according to the explanation of "INP" in AMBER manual,
should I set SURFTEN=0.0072, SURFOFF=0.0 in both MM/GBSA and MM/PBSA ?
Q3.
Do I need any other settings?
Best regards,
WATANABE
> 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
>>
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--
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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
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Received on Thu Sep 12 2013 - 19:30:02 PDT
