Hi Dave,
>> PS: I can’t find the pysander documentation, so if anyone knows where it
>> is please let me know.
>
> Please see Section 17.13 in the Amber 2017 Reference Manual.
>
> Although various pages in the Manual refer to pysander (and to pytraj),
> neither of these are actually programs: rather they refer to python import
> modules. Somewhat confusingly, the import library is called "sander", not
> "pysander”.
Your clarification is very helpful - I think I just overlooked that section of the manual. The manual is a bit long and I might have just been searching for the word “pysander”, which only brings up a few hits outside of that section. I understand “pysander” / pytraj are Python APIs and not standalone programs, and what we call “pysander” is just “import sander”.
Incidentally, because the manual is long, I tend to split the PDF into sander and cpptraj-specific chapters to make it more searchable. :)
> (Lee-Ping: since you already know about "import sander", I don't think you
> have anything more to learn....)
>
> (Hai, Jason: please correct the above if I am wrong. But if someone as
> experienced as Lee-Ping is getting confused, this suggests we should really
> fix up the manual. If you do a search on "pysander" in the Manual, there are
> a number of hits that seem to suggest that pysander and pytraj are programs.
> And note that seemingly similar things like pytleap and pymdpbsa really *are*
> standalone python drivers.)
I blame myself for reading the instructions carefully enough. It might be nice to include a sentence with the word “pysander” keyword in section 17.13.
Thanks,
- Lee-Ping
> ....dac
>
>
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Received on Tue Feb 13 2018 - 11:00:02 PST
