Hi Jason,
I have had the same problem (i.e. GB energy of ligand binding (-)ve and PB (+)ve. Setting inp=1, throws out the following warnings:
Warning: inp=1 was old default
Warning: cavity_surften=0.0378 not recommended for inp=1, switching to inp=1 default value: 0.0050
Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to inp=1 default value: 0.000
my mmpbsa input file is:
Input file for running PB and GB
&general
interval=2, endframe=2000, verbose=1,
# entropy=1,
/
&gb
igb=2, saltcon=0.100
/
&pb
inp=1, istrng=0.100,
/
Any explanation for this would be much appreciated. What other settings are needed to overcome this problem?
Best regards
George
On Mar 24, 2014, at 9:15 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, 2014-03-24 at 09:28 +0530, Arunima Shilpi wrote:
>> Dear Sir
>>
>> I followed the tutorial for MMGBSA and MMPBSA binding energy calculation.
>> Here the binding energy for MMGBSA comes to be negative whule for MMPBSA
>> comes to be positive.
>>
>> I request you to kindly guide me as to how to include the entropy papramter
>> in the calculation of binding energy.
>>
>> While going through the mailing list I got the following option
>>
>> "To be comparable with the GB, you'll need to set inp=1, i.e. without
>> the EDISPER".
>>
>> Here I dint get how to edit this parameter in mmpbsa.py file.
>
> Did you look at the manual? On page 356 of the AmberTools manual it
> lists the variables that belong in the &pb namelist, and inp is one of
> them.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Mon Mar 24 2014 - 08:30:04 PDT
