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**Describe the issue**
I performed charm36 ff based MD simulation using Gromacs 2018.1. I am able to calculate g_mmpbsa based binding energy calculations.
**_If you will report an error, please co…
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Thank you for working to extend this useful tool to divalent atoms. When attempting to plot the levels of Ca40 using calc.makeLevels(4,50,0,1,sList=[0]), I do not see the ground state that I would e…
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I have been using ChEBI "X molecular entity", especially in assay modelling, as a shorthand for saying X atom or X ion.
I'm thinking now that that's misguided. When @cstoeckert and last reviewed s…
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PLEASE ATENTION!
It work well at v1.2.0, untill I updated gmx_MMPBSA by:
`pip install gmx-MMPBSA --upgrade`
protein_forcefield="oldff/leaprc.ff99SBildn"
gmx_MMPBSA v1.3.1 based on MMPBSA version…
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**Describe the issue**
gmx_MMPBSA installation issue
**_If you will report an error, please complete this form_**
**To Reproduce**
```
$source home/byun/apps/AMBER/amber20_src/amber.sh
$conda …
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I reinstalled amber20 with miniconda3 and python3
But I have encountered another problem and below is the gmx_MMPBSA.log
```
[INFO ] Started
[INFO ] Loading and checking parameter files for…
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I've attempted to test whether the current toolkit can recreate the `System`s we used for the hydration free energy calculations in the SMIRNOFF paper. Currently, the test fails for molecule `1019269`…
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Christopher Bayly and I have been thinking that perhaps we should, at this stage, build in the infrastructure for off-center charges ("lone pair", sigma hole) into the SMIRFF format before we get to p…
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As part of the ongoing evolution of the [SMIRNOFF SMARTS-based forcefield specification scheme](https://github.com/open-forcefield-group/smirnoff/blob/master/The-SMIRNOFF-force-field-format.md), there…
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In connection with the Mobley Group undergraduate project [off-ffcompare](https://github.com/MobleyLab/off-ffcompare) I've been looking at how SMIRNOFF99Frosst types the molecules in DrugBank. Below I…