Fix bug for nbfix/chamber in ParmEd v3.4 (#1282)

* Fix bug for nbfix/chamber in ParmEd v3.4 * Remove visualization tests
ParmEd · Jan 17, 2023 · d0fa4b6 · d0fa4b6
1 parent 1742bae
commit d0fa4b6
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Showing 3 changed files with 4 additions and 57 deletions.
diff --git a/.github/workflows/Test.yaml b/.github/workflows/Test.yaml
@@ -28,6 +28,8 @@ jobs:
         python-version: ${{ matrix.python-version }}
         environment-file: devtools/environment-dev.yaml
         activate-environment: parmed-dev
+        channels: conda-forge,bioconda
+        # mamba-version: "*"
 
     - name: Environment Information
       shell: bash -l {0}

diff --git a/parmed/amber/_chamberparm.py b/parmed/amber/_chamberparm.py
@@ -579,10 +579,10 @@ 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

diff --git a/test/test_parmed_visualization.py b/test/test_parmed_visualization.py