Merge pull request #101 from openmm/adding-systems

[WIP] Adding all JACS systems to the repo
openmm · Apr 7, 2020 · bd2f809 · bd2f809
2 parents 04efd68 + 5bae89c
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diff --git a/openmmforcefields/data/perses_jacs_systems/bace/Bace_ligands_shifted.sdf b/openmmforcefields/data/perses_jacs_systems/bace/Bace_ligands_shifted.sdf
diff --git a/openmmforcefields/data/perses_jacs_systems/bace/Bace_protein.pdb b/openmmforcefields/data/perses_jacs_systems/bace/Bace_protein.pdb
diff --git a/openmmforcefields/data/perses_jacs_systems/bace/README.md b/openmmforcefields/data/perses_jacs_systems/bace/README.md
@@ -0,0 +1,3 @@
+### Bace setup
+
+TLA spectator molecule was saved as an `.sdf` from `*merged.pdb` file, and manually edited to add bonds and charges for the two carboxylic acid groups.
diff --git a/openmmforcefields/data/perses_jacs_systems/bace/TLA.sdf b/openmmforcefields/data/perses_jacs_systems/bace/TLA.sdf
@@ -0,0 +1,39 @@
+TLA
+  PyMOL2.3          3D                             0
+
+ 14 13  0  0  0  0  0  0  0  0999 V2000
+   51.0480   41.7530   16.8360 C   0  0  0  0  0  0  0  0  0  0  0  0
+   51.7480   42.7370   16.7270 O   0  0  0  0  0  0  0  0  0  0  0  0
+   49.9970   41.4790   15.7710 C   0  0  0  0  0  0  0  0  0  0  0  0
+   50.5830   41.4510   14.4170 O   0  0  0  0  0  0  0  0  0  0  0  0
+   48.8520   42.5320   15.8660 C   0  0  0  0  0  0  0  0  0  0  0  0
+   47.7150   42.1050   15.0570 O   0  0  0  0  0  0  0  0  0  0  0  0
+   48.4150   42.8410   17.3130 C   0  0  0  0  0  0  0  0  0  0  0  0
+   47.7010   42.0800   17.9430 O   0  0  0  0  0  0  0  0  0  0  0  0
+   51.1340   41.0190   17.7870 O   0  0  0  0  0  0  0  0  0  0  0  0
+   48.8500   43.9070   17.8270 O   0  0  0  0  0  0  0  0  0  0  0  0
+   51.0010   40.5780   14.3160 H   0  0  0  0  0  0  0  0  0  0  0  0
+   47.0520   41.8980   15.7380 H   0  0  0  0  0  0  0  0  0  0  0  0
+   49.5510   40.5280   16.0860 H   0  0  0  0  0  0  0  0  0  0  0  0
+   49.2120   43.4960   15.4850 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  3  1  0  0  0  0
+  1  2  2  0  0  0  0
+  3  4  1  0  0  0  0
+  3  5  1  0  0  0  0
+  3 13  1  0  0  0  0
+  4 11  1  0  0  0  0
+  5  6  1  0  0  0  0
+  5  7  1  0  0  0  0
+  5 14  1  0  0  0  0
+  6 12  1  0  0  0  0
+  7  8  2  0  0  0  0
+  7 10  1  0  0  0  0
+  1  9  1  0  0  0  0
+M  CHG  1   9  -1  
+M  CHG  1   10  -1  
+M  END
+>  <pdb_header>
+CRYST1   70.419   72.124   66.012  90.00  90.00  90.00 P 1            
+
+
+$$$$
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		### Bace setup

		TLA spectator molecule was saved as an `.sdf` from `*merged.pdb` file, and manually edited to add bonds and charges for the two carboxylic acid groups.