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I am using charmm27 force filed.
For simulation.context.getState(getEnergy=True,groups=0).getPotentialEnergy() and simulation.context.getState(getForces=True,groups=0).getForces(), they should give en…
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@peastman @jchodera @swails
**tl:dr**: All protein/nucleic converted, some issues outstanding that could bring in a few more FFs, some FFs never to be converted - all explained below. See ions & sol…
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```
alexxy@xeon /misc/_Work/acpypi $ ./acpype.py -i benz.pdb
================================================================================
===============
| ACPYPE: AnteChamber PYthon Parser inter…
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```
alexxy@xeon /misc/_Work/acpypi $ ./acpype.py -i benz.pdb
================================================================================
===============
| ACPYPE: AnteChamber PYthon Parser inter…
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Was trying to solvate a system I made in Rosetta, using the AMBER99SBildn forcefield in OpenMM, when I got this error:
``` python
In [82]: mod = solvate(s.positions, s.topology, ff, 0.1, padding=1.0,…
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@jchodera @swails
I swear nightmares about dihedrals will keep me awake at night forever after this...
RNA test system - cleaned up 5C5W:https://gist.github.com/rafwiewiora/686a17b8004414fe5562
Fa…
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Here is the data from x3dna
``` bash
Minor and major groove widths: direct P-P distances and refined P-P distances
which take into account the directions of the sugar-phosphate backbones
(Subt…
hainm updated
8 years ago
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I've just compared cpptraj and x3dna output. So far the helical pars match very well. But cpptraj skips 0.0 values for `X-disp Y-disp h-Rise Incl. Tip h-Twist` in Dataset. Is this you…
hainm updated
9 years ago
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```
even though the check is meant for nucleic acids only:
From check.db:
ID : model_000.pdb
CheckID : PL3CHK
Program : WHAT IF
Version : 6.0 (20080412-0930)
Text : Side chain planar…
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what do you think to add more to this?
https://github.com/ParmEd/ParmEd/blob/d831c5a45053cd6298ec61ca7a8d1f7cfabbd768/parmed/residue.py#L266-L276
hainm updated
9 years ago