By the way you can use the "continue" mode to avoid re-equilibrating all
the previous windows.
Best,
Jane
On Tue, Nov 28, 2017 at 3:25 AM, Maura Malinska <mmalinska.chem.uw.edu.pl>
wrote:
> Dear All,
>
> I am using an apr.py script for APR method in CHCl3. Host is a
> calix[6]arene with different guests. I am working now with a piridine
> guest. The simulation are currently at the equilibrium stage. It went
> smoothly up to the p16 window. I have got this error:
>
> Traceback (most recent call last):
> File "apr.py", line 1210, in <module>
> main()
> File "apr.py", line 1185, in main
> this.run_setup()
> File "apr.py", line 927, in run_setup
> self.prepare_and_simulate('translation')
> File "apr.py", line 464, in prepare_and_simulate
> apr_solvate.setup_solvate(self.warning, self.solvent_model,
> self.num_solvent, self.ions, self.amber16)
> File "/net/scratch/people/plgmauram/cb6_pir/apr_solvate.py", line 119,
> in setup_solvate
> if manual_removal is not None:
> UnboundLocalError: local variable 'manual_removal' referenced before
> assignment
>
> I have attached the apr.in file. Could someone help me?
>
> Thank you
>
> --
> Maura Malinska
> Research Associate
> Faculty of Chemistry
> University of Warsaw
> ul. Ludwika Pasteura 1, 02-093 Warsaw, Poland
>
> tel. 22 55 26 356
> mmalinska.chem.uw.edu.pl
>
> www.uw.edu.pl,
> http://crystal.chem.uw.edu.pl/staff/malinska.html
>
>
> _______________________________________________
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>
>
--
Dr. Jian (Jane) Yin
Postdoctoral Researcher
3117 Gilson Lab Office
Skaggs School of Pharmacy and
Pharmaceutical Sciences, UCSD
9500 Gilman Dr., La Jolla, CA 92093-0736
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Received on Tue Nov 28 2017 - 15:30:03 PST
