Qinghua,
Can you stay with Ambertools and use the python script? It has more
control of input and the default is to set PB and GB calculations with
the same input parameters.
All the best,
Ray
On Sun, Nov 20, 2011 at 7:34 AM, Qinghua Liao <fantasticqhl.gmail.com> wrote:
> Dear Ray,
>
> Thanks very much that you can give me an answer on Sunday. I am sorry for
> not telling you that I used amber11 together with ambertools-1.5 to do the
> calculation. For the parameters, I used the default ones in the first
> calculation. That's the point confusing me, how can this happen? How can I
> figure it out? Thanks very much!
>
>
> Best Regards,
>
> Qinghua
> Ph.D. student
> Juelich Research Center
>
>
> On Sun, Nov 20, 2011 at 4:00 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>
>> Dear Qinghua,
>>
>> For one thing, your PBSUR and GBSUR are already different -57.5 vs
>> -9.7.Apparently you are using different parameters between the two
>> models.
>>
>> Maybe I shall recommend using the latest Ambertool so it's easier to
>> trace down your problem in the setup?
>>
>> All the best,
>> Ray
>>
>> On Sun, Nov 20, 2011 at 12:10 AM, Qinghua Liao <fantasticqhl.gmail.com>
>> wrote:
>> > Dear amber users,
>> >
>> > I did a binding free energy of a ligand to a protein using mm_pbsa.pl,
>> here
>> > is the result:
>> >
>> > # DELTA
>> > # -----------------------
>> > # MEAN STD
>> > # =======================
>> > ELE -67.88 7.84
>> > VDW -66.86 3.92
>> > INT -0.00 0.00
>> > GAS -134.74 8.89
>> > PBSUR -57.52 1.98
>> > PBCAL 115.17 9.15
>> > PBSOL 57.64 9.07
>> > PBELE 47.29 8.98
>> > PBTOT -77.10 9.24
>> > GBSUR -9.67 0.33
>> > GB 160.07 21.87
>> > GBSOL 150.40 21.87
>> > GBELE 92.20 22.30
>> > GBTOT 15.66 22.00
>> >
>> > I am wondering why PBTOT can be -77.10 while GBTOT be 15.66, I think it
>> > does not make sense. So how should I explain such a situation? Thanks
>> very
>> > muc!
>> > --
>> > Best Regards,
>> >
>> > Qinghua
>> > Ph.D. student
>> > Juelich Research Center
>> > _______________________________________________
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>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
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Received on Mon Nov 21 2011 - 10:30:03 PST
