Dear WATANABE,
Please see my replies below after your questions.
Ray
>
> 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?
You can only use LCPO for GBSA to compute SASA for nonpolar solvation
free energy by setting MS=0. If you read the comments in "mm_pbsa.in"
in the mmpbsa/Example directory, MS=0 for PBSA means to use the pbsa
routine in sander to compute SASA. The pbsa routine computes SASA
analytically, i.e. it is more closely related to the MOLSURF method by
setting MS=1. LCPO is an pairwise-approximated method of the gbsa
routine in sander. If you insist on setting MS=0, the closest PBSA
option is to set INP=1 and use the same SURFTEN and SUROFF values as
those for the GBSA calculation.
>
> 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 ?
Yes, you should set them to be same between GBSA and PBSA. Also, why
not using MOLSURF by setting MS=1? MOLSURF is quite fast, besides LCPO
is only approximated. If you use LCPO for GBSA and MOLSURF for PBSA,
your two free energies are clearly different and harder to compare. Of
course, you can certainly match up LCPO nonpolar solvation free
energies by hand outside the script.
>
> Q3.
> Do I need any other settings?
Just a general comment ... I'm not saying this for you to reproduce
the paper's setting.
if you want the best consistency between GBSA and PBSA calculations,
you may want to set radiopt=0 instead of radiopt=1 for PBSA so that
the same set of radii are used between the two methods. If you want to
play with all the options, try to play with them consistently, i.e.
using the same options and inputs for both GBSA and PBSA.
All the best,
Ray
>> 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
> www.hpc.co.jp
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Received on Fri Sep 13 2013 - 12:00:02 PDT
