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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Received on Tue Mar 13 2012 - 15:30:03 PDT
