We prefer changing the manual instead. Qin, can you work with Jason on
this? The defaults were changed for more stable numerical behaviors.
Ray
On Thu, Apr 19, 2012 at 1:56 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Apr 19, 2012 at 4:40 PM, Niel Henriksen <niel.henriksen.utah.edu>wrote:
>
>> Hi,
>>
>> Just a heads up. It looks like the defaults for MMPBSA.py don't match
>> what the manual says.
>>
>> For this input:
>>
>> &general
>> receptor_mask=':1-38', ligand_mask=':39', interval=1,
>> verbose=1, keep_files=0, entropy=0, netcdf=1, use_sander=0,
>> /
>> &pb
>> /
>>
>
> You're right. The latest changes to the PB defaults were not accompanied
> by changes to the manual. Should we issue a patch to make the code
> compatible with the manual, or should we publish errata somewhere to
> 'update' the manual with the code (assuming anybody reads those)?
>
> Thanks!
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Thu Apr 19 2012 - 14:30:03 PDT
