Hi Qin,
Thanks for this. I appreciate your time.
Best,
Jesper
On Mar 13, 2012, at 4:46 PM, Qin Cai wrote:
> Hi Jesper,
>
> On Mar 13, 2012, at 3:58 PM, Jesper Sørensen wrote:
>
>> Hi Qin,
>>
>> Thanks for getting back to me so quick. That makes more sense looking at the results.
>>
>> So if I want to calculate with the vdW surface definition, sprob=0 is the more appropriate value, because this sets both sprob and dprob to 0 (like what I manually did in A)?
>
> Yes, exactly.
>>
>> How about for the SE surface, should I define dprob=1.4, sprob=1.6 (like D)? Then sprob is 0.2 higher than dprob in the SE surface results, but is it then okay to be equal (both 0) for the vdw surface results?
>
> The dprob option is used for polar solvation calculation and sprob is used for nonpolar components. It's okay that you have two sets of parameters for two surface definitions. Default sprob is set to 1.6 for backward compatibility and probably not the optimal one for your case. These two papers can give you some insights into the parameter optimization of the nonpolar solvation model.
>
> Wagoner, J. A.; Baker, N. A., Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms. Proc. Natl. Acad. Sci. U. S. A. 2006, 103 (22), 8331-8336
> Tan, C.; Tan, Y. H.; Luo, R., Implicit nonpolar solvent models. J. Phys. Chem. B 2007, 111, 12263-12274
>
> Thanks,
> Qin
>
>>
>> Best,
>> Jesper
>>
>>
>>
>> On Mar 13, 2012, at 3:13 PM, Qin Cai wrote:
>>
>>> In AT 1.5, dprob and sprob are defined this way: default sprob is 1.6; default dprob is equal to sprob; when dprob is set to 0, it'll be reset to be equal to sprob.
>>>
>>> So in Jesper's tests, the real dprob and sprob values are
>>>
>>> dprob sprob
>>> A 0 0
>>> B 1.4 1.4
>>> C 1.4 1.4
>>> D 1.4 1.6
>>> E 1.6 1.6
>>>
>>> The sprob could affect the dprob value, but the EPB is computed with dprob only. So B, C, and D has same EPB since same dprob is used.
>>>
>>> Best,
>>> Qin
>>> On Mar 13, 2012, at 2:11 PM, Ray Luo, Ph.D. wrote:
>>>
>>>> I'm forwarding this to Qin to answer ...
>>>>
>>>> Ray
>>>>
>>>>
>>>> ---------- Forwarded message ----------
>>>> From: Jesper Sørensen <jesorensen.ucsd.edu>
>>>> Date: 2012/3/13
>>>> Subject: [AMBER] PBSA sprob question
>>>> To: AMBER Mailing List <amber.ambermd.org>
>>>>
>>>>
>>>> Hi all,
>>>>
>>>> I have been trying to understand the EPB value in terms of different
>>>> surface definitions, the vdW or SE.
>>>>
>>>> To change the surface definition I have used the dprob variable.
>>>> For vdW dprob=0
>>>> for SE dprob=1.4
>>>>
>>>> My question is now what should the sprob value be and what does it affect?
>>>> In the AmberTools 1.5 manual it states that the sprob value is (in
>>>> this version) is used to calculate the dispersion term and potentially
>>>> also the cavity term.
>>>> Neither of these values should be part of the EPB value, correct?
>>>>
>>>> I've done some tests...
>>>>
>>>> dprob sprob EPB
>>>> A 0 0 191 kcal/mol
>>>> B 0 1.4 234 kcal/mol
>>>> C 1.4 1.4 234 kcal/mol
>>>> D 1.4 - 234 kcal/mol
>>>> E 0 - 239 kcal/mol
>>>>
>>>> In D and E I have let sprob be undefined, which means it should go
>>>> back to default values. In the log file I cannot see what that default
>>>> value is, but apparently it is not 0 (zero) or 1.4 in the case of the
>>>> dprob=0, when you compare A, B and E.
>>>> When dprob=1.4, it seems likely that sprob could default to 1.4, when
>>>> comparing C and D, but I am not sure this is true.
>>>> Again, should sprob even affect the EPB value?
>>>>
>>>> I hope you can help me understand this parameter better.
>>>>
>>>> Best regards,
>>>> Jesper
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>
>>
>>
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Received on Wed Mar 14 2012 - 09:00:05 PDT
