Ahh ... good. Thanks for the help.
--Niel
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Monday, October 03, 2011 8:48 PM
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA input error for INP
On Mon, Oct 3, 2011 at 10:33 PM, Niel Henriksen <niel.henriksen.utah.edu>wrote:
> I'm doing some simple testing with MMPBSA after bugfixing and
> re-installing amber11 and ambertools1.5 (with intel).
>
> I get the following error regarding the INP value:
>
> Reading command-line arguments and input files...
> Input Error: INP/NPOPT (1) must be either 0, 1, or 2!
>
> Here is my input file:
>
> &general
> receptor_mask=':1-38', ligand_mask=':39', strip_mdcrd=0,
> verbose=1, keep_files=1, entropy=0, netcdf=1,
> /
> &pb
> radiopt=0, istrng=200, inp=1,
> /
>
>
> MMPBSA dies for any specified value of inp (0,1, or 2). If I
> leave it blank, then it runs fine. I was thinking this was some
> type of integer -> floating point mix up,
integer -> string mix-up, actually, but yea.
> but the radiopt
> keyword doesn't have a problem and it has the exact same
> error checking code (in utils.py).
>
> I can get around this using the "-make-mdin" method, I think.
>
Yep, that will work.
>
> But I can't tell if my computer is going crazy, or if I am, .... or both.
>
Not going crazy. It was never cast to an integer (ignore the fact that
python doesn't support typecasting in the strict compsci definition of the
word). Therefore, it was comparing your input as a string to the integers
0, 1, and 2 (so it was obviously never working).
You are apparently the first person to have tried specifying inp in the
input file :). (It defaults to an integer 1, which is why it never failed
when you didn't specify it).
I've fixed the issue and it should be a bugfix shortly. For the time being,
just apply the attached fix (no need to use patch, just hack it into
MMPBSA.pypp and reinstall it).
The upcoming version of MMPBSA.py has a completely reworked input parser
that does type-checking as it parses (as well as a number of other much
better features/designs).
In any case, thanks for the report!
Jason
> Thanks for any help,
> --Niel
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Oct 03 2011 - 20:00:08 PDT
