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Hi there,
I want to get gromacs topology file from OpenMM simulation.
**My code-**
smirnoff = SMIRNOFFTemplateGenerator(forcefield='openff-2.0.0.offxml')
sdf_files = ['bcd_gly.sdf', 'aspi…
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In #357 we decided to use distance cutoffs as a proxy for determining 1-3 and 1-4 pairing.
A more precise way to determine this is using the adjacency matrix described in that issue. The implementati…
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DeepChem Version: 2.1.0
Platform: OS; python 3.5
I have trained a Grid-Random Forest regression model on the PDBBind core dataset that has been featurized with the grid featurizer (loaded disk dat…
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Hi!
I've been setting up a few mutants to study the impact of a mutation in the context of a dimerization, and I have encountered a mutation case that appears to fail? It is an ILE->ASP mutation.
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Would it be interesting to implement those in rdkit:
https://pubs.acs.org/doi/suppl/10.1021/acs.jcim.8b00684/suppl_file/ci8b00684_si_001.pdf
These are the supplementary materials of:
All in One…
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I have a use case of BioSimSpace that takes an SDF as input, parameterises the molecule using the GAFF forcefield, writes out just a grotop file. In truth, I do write a PDB file too but I want to only…
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Hey everyone,
I'm new to Python and OpenMM. I'm trying to use custom nonbonded force and define parameters for each pair rather than per atom. I've written a Python script to generate a forcefield.…
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**Describe the bug**
I want to do a constrained minimization. but sometimes, it failed. After trouble shooting, I found the forcefild energy and grad were nan. How to solve it? the following are my c…
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OpenMM 8.1 has a performance improvement for larger systems: https://github.com/openmm/openmm/pull/4147.
I attempted to port it myself but was unsuccessful. [findInteractingBlocks.hip](https://gith…
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Would there be interest in an H5MD reporter for OpenMM? Simple but effective format based on HDF5.
It is well documented (https://www.nongnu.org/h5md/index.html, https://www.sciencedirect.com/scie…