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Fix bug reported by Alex Sodt #1281

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merged 2 commits into from
Jan 17, 2023
Merged

Fix bug reported by Alex Sodt #1281

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a874f40
Fix bug reported by Alex Sodt
swails Jan 17, 2023
f710f55
Turn off mamba since it's glitchy right now
swails Jan 17, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/Test.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ jobs:
environment-file: devtools/environment-dev.yaml
activate-environment: parmed-dev
channels: conda-forge,bioconda
mamba-version: "*"
# mamba-version: "*"

- name: Environment Information
shell: bash -l {0}
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4 changes: 2 additions & 2 deletions parmed/amber/_chamberparm.py
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Expand Up @@ -559,10 +559,10 @@ def _set_nonbonded_tables(self, nbfixes=None):
for i, fix in enumerate(nbfixes):
for terms in fix:
j, rmin, eps, rmin14, eps14 = terms
i, j = min(i, j-1), max(i, j-1)
k, l = min(i, j-1), max(i, j-1)
eps = abs(eps)
eps14 = abs(eps14)
idx = data['NONBONDED_PARM_INDEX'][ntypes*i+j] - 1
idx = data['NONBONDED_PARM_INDEX'][ntypes*k+l] - 1
data['LENNARD_JONES_ACOEF'][idx] = eps * rmin**12
data['LENNARD_JONES_BCOEF'][idx] = 2 * eps * rmin**6
data['LENNARD_JONES_14_ACOEF'][idx] = eps14 * rmin14**12
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