Re: [AMBER-Developers] MMPBSA.py defaults

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Thu, 19 Apr 2012 14:27:15 -0700

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
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers

_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Thu Apr 19 2012 - 14:30:03 PDT
Custom Search