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  1. 18 May, 2015 1 commit
  3. 02 May, 2015 1 commit
  5. 10 Apr, 2015 1 commit
    • Jason Swails's avatar
      Improve CHARMM parsing when resnums have inscodes · 7b30da6e
      Jason Swails authored 
      Apparently CHARMM PSF files (particularly those printed by VMD's psfgen) can
have an insertion code tacked on to the end of the residue number, meaning that
casting to an integer will invariably fail.  We can't just ignore the insertion
code, though, since it will differentiate from the residues that came before and
after (which will likely have the same number -- same general idea as insertion
codes from PDB files). So instead we pull the insertion code off of the residue
number and extend the Residue object to accommodate that.

This is the port of the fix from ParmEd: ParmEd/ParmEd#98

I added a test for this case.
      7b30da6e
  7. 19 Mar, 2015 1 commit
  9. 05 Mar, 2015 1 commit
  11. 11 Feb, 2015 1 commit
  13. 09 Feb, 2015 1 commit
  15. 07 Feb, 2015 1 commit
  17. 19 Jan, 2015 2 commits
  19. 23 Oct, 2014 2 commits
  21. 21 Jul, 2014 1 commit
  23. 17 Jul, 2014 1 commit
  25. 11 Jul, 2014 1 commit
    • Jason Swails's avatar
      Add NBFIX support to the Amber topology file parsers. The new Amber ff14IPQ · d865c202
      Jason Swails authored 
      force field utilizes nbfix functionality. Without this commit, using a ff14IPQ
topology file (or one modified by ParmEd to contain off-diagonal LJ elements),
would happily run, but ignore off-diagonal elements.

The new Chen and Garcia RNA force field (see doi:10.1073/pnas.1309392110) also
utilizes off-diagonal terms in its parametrization scheme.

One shortcoming is that the approach taken here -- using a pair parameter lookup
table -- cannot be currently used with a long-range correction because it is not
a `Continuous1DFunction' by virtue of using two `Discrete2DFunction'
TabulatedFunction classes.

Energies here match the values obtained with Amber to 0.01 -- 0.1 kcal/mol
(within 0.1% of the total).
      d865c202
  27. 02 Jul, 2014 1 commit
  29. 27 Jun, 2014 1 commit
  31. 28 May, 2014 1 commit
  33. 21 May, 2014 1 commit
  35. 04 May, 2014 1 commit
  37. 10 Apr, 2014 1 commit
    • Jason Swails's avatar
      Add a couple unittests for CHARMM files. Good thing, too, because they helped · 31f09353
      Jason Swails authored 
      pick up some bugs that were not caught in my initial test following the port
from ParmEd.

All 4 tests pass right now, although no periodic systems are being tested.
Currently CHARMM, XPLOR, and VMD tests are all being run (for the same ala-3
system).

Disable implicit solvent tests, since there is no robust radii assignment
routine yet (the radii are stored in the Amber topology file).  I will port my
assignment routine from ParmEd here shortly and then re-enable the GB tests.
      31f09353
  39. 02 Oct, 2013 1 commit
  41. 01 Aug, 2013 1 commit