On Fri, May 3, 2013 at 5:53 AM, Jan-Philip Gehrcke
<jgehrcke.googlemail.com>wrote:
> On 04/30/2013 03:05 PM, Jan-Philip Gehrcke wrote:
> > So, while we are waiting for someone to comment on this who is more
> > familiar with PBSA [...]
>
> It looks like this issue is being taken care of, thanks to Qin and Ray.
>
> Jason, there is one small issue with the output in
> FINAL_RESULTS_MMPBSA.dat when using inp=1. In the sections for complex,
> receptor, and ligand only "ENPOLAR" appears. In the "differences"
> section, also EDISPER appears, with a value of 0.
>
The values of EDISPER are suppressed when they are equal to zero (not sure
why it isn't in the DELTA section -- I'll check on that). EDISPER was
added as a placeholder well before inp=2 became the default SA model (and
EDISPER is only non-zero when inp=2).
> Also, I have seen in the code that there is a print_summary_csv() method
> somewhere whose purpose seems to be to write the same information as in
> FINAL_RESULTS_MMPBSA.dat to a CSV file -- but from the docs and from the
> code I was not able to find the external interface to this method. Do
> you have plans to provide the results in FINAL_RESULTS_MMPBSA.dat in a
> machine-readable output file (not surprisingly the
> FINAL_RESULTS_MMPBSA.dat 'format' itself has changed between MMPBSA.py
> versions...)?
>
The CSV format for the standard output was an idea initially, then I
decided against it since a large amount of the information printed in the
output file is not really data, but more just information about the
calculation. As a result, I never implemented the summary CSV file. The
decomposition results, on the other hand, are almost entirely data, so
those have been implemented in CSV format. So too have the energy dumps
(-eo and -deo flags). If there's general interest in a particular feature,
I can work on that for the next release.
I haven't changed the actual format of the output appreciably since the
original version 3 to 4 years ago. I have added new terms as they became
necessary (like improper, urey-bradley, and CMAP terms for chamber
topologies, the SCF terms for QM/MM, the RISM solvation terms, EDISPER,
etc.), but hopefully nothing that breaks existing parsers (am I wrong here?)
On the other hand, there's a new API (not _really_ an API, but an easy way
to extract data from the _MMPBSA_ intermediate files into your own python
script with a single function call) so you can do your own types of data
analysis in Python using the numpy/scipy machinery (documented in the
AmberTools 13 manual).
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri May 03 2013 - 07:30:03 PDT
