[MMTK] HarmonicDihedralRestraint problems

Qadir Timerghazin qadir.timerghazin at gmail.com
Wed Apr 15 15:27:17 UTC 2009


> Ah, I see - that's in fact due to a bug in MMTK. Your script has two
> assignments to universe.molecule. The second one should overwrite the first
> one so that there is only one molecule in the end. I fixed this bug, so your
> water script will not work with future MMTK releases. You should use
> different attributes for each molecule:

Yes, I actually was quite surprised this notation was adding a
molecule instead of overwriting.

>> FF modification file, which is inconvenient to post. Below is a
>> protein example, which segfaults with the dihedral constraint.
>
> That was in fact a trivial typo that was easy to fix. The fix will be in
> future releases, but you can apply the attached patch file to your current
> release as well.

Great - it works now! Thank you very much, Konrad!

Cheers,
Qadir

--
Dr. Qadir K. Timerghazin,
NSERC Postdoctoral Fellow

Department of Chemistry
University of Waterloo
200 University Avenue West
Waterloo, ON, Canada N2L 3G1



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