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I am trying to incorporate non-canonical amino acids by the applyMutation() function. Is there a protocol to achieve this?
The pdb is added in the template library and also in the 'proteinResidues'…
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OpenMM's topology objects and readers/writers don't provide enough chemical information to actually parameterize small molecules nonstandard biopolymers, post-translational modifications, glycosylatio…
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For forcefields such as tip4p, we can read the forcefield, and virtual sites are treated just the same as a site. The virtual site is then assigned an atomtype just the same via the forcefield, and th…
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**Is your feature request related to a problem? Please describe.**
We're looking at using Sage in relation to a project on electrolyte design for li-ion batteries. Currently the force field doesn't h…
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The docstring for `getFreeEnergyDifferences()` says of `uncertainty_method`:
```
uncertainty_method : string, optional
| Choice of method used to compute asymptotic covariance method,…
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Hey guys,
I was recommended to post this issue here by @jchodera.
I've been trying to use openmmtools' alchemy.py code to compute solvation free energies of an ethanol molecule in water. The mai…
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Those of us in the MD community would very much like to be able to take output from QM packages and take it directly into MD engines and chemistry toolkits we use. However, these typically require wha…
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Currently the RJMC algorithm gives the result that the one parameter model is justified only in a 3:1 ratio. We expected that the one parameter model (just epsilon) would always be favored because we …
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I am trying to use the Perses CLI to calculate free energies for nucleotide binding to the IP3 receptor and am using ATP AMP as a test run. I've been able to successfully run Perses for the Tyk2 exam…
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Lepton has the ability to compute dU/dr for force evaluation. This feature request is to allow users to take derivative to arbitrary variables (or a specified set) in the energy expression to compute …