Hi David,
I don't think I've ever tried the PB interface through the sander API. Do
you have an example script that shows the error you're seeing?
Thanks,
Jason
On Sat, Mar 19, 2022 at 6:34 PM David Poole <thepoole.ucdavis.edu> wrote:
> I found success in getting it installed using conda forge independently of
> my amber/ambertools installation. I am unsure why it didn't work off the
> bat as parmed.py and pytraj both worked (mostly), and even pamred.py
> allowed me to use esander. I think it was just a matter of the version
> included in ambertools?
>
> If there are opportunities to help clean up github documentation, maybe the
> community could help more as well? That might be a good thing to push as
> well.
>
> Alas now that things are working, I have a bug to report: While I can use
> esander in pytraj to do gb (igb > 0) and pme calculations, when I attempt
> to do two or pb calculations (ipb > 0 or igb = 10), I get a
> segmentation fault from pb_init() and the program exits. The minimum
> example is computing the single point pb for any two loaded structures in
> pytraj. Calculations can be set up with either mm_options (options.ipb > 0,
> or igb = 10) or by setting igb in the esander method (igb = 10), which all
> lead to the same result. This would be particularly useful for my new
> workflows for mmxbsa calculations using the pytraj interface.
>
> Kindly,
> David
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 01 2022 - 15:30:02 PDT
