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**Is your feature request related to a problem? Please describe.**
Gasteiger charges sometimes do not agree between rdkit, AmberTools/antechamber, and OpenBabel. The importance of this is debatable, …
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During #151, it was decided that the `basis` field in `AtomicInput` for the `OpenMMHarness` need not be specified. When not specified, it would be generated from the contents of `url` or `offxml`. Thi…
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Hi there!
First thank you for your great work here!
I'm a newcomer to openmm and currently try to set up an MD simulation of a protein with a small non-standard ligand using GAFF. To get starte…
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Hi,
I'm preparing a glycoprotein using tleap and glycam06j/ff14SB. Since I want to simulate in gromacs I used ACPYPE (the :latest docker image recipe built with Singularity last week). I also used …
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Hiya,
I'm rebuilding the topologies from the TIES paper but I'm having trouble with l20-l21 for CDK2. I end up with a weird ring in the final topology. I've started from the Wang 2015 input ligands…
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#37 showed that the current way of managing AmberMini is not sustainable and we will need a new strategy.
Based on feedback from #37, it should be possible to compile the parts of AmberTools that we …
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As a YANK newbie, it seems the existing ligand parameterization pipeline doesn't use any ab initio QM calculations.
Since Schrodinger runs their force field builder and Jaguar to fill in missing to…
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I installed the latest yank (0.25.2) and tested it using the scripts given in t4-lysozyme example directory.
1) The first question is:
When I increase "default_number_of_iterations" from 500 to 20…
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This is very likely a niche issue (my very sloppy work found this error), but it may be worth sanitizing .mol2 files during setup--
If the substructure id for a atom in a mol2 file matches the file…
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Can MolModMT include a method to predict the propensity of a given sequence segment to form secondary structures? Something similar to what [APSSP server](http://crdd.osdd.net/raghava/apssp/) does, or…