Merge pull request #95 from jchodera/master

Update Src testsystems
choderalab · Sep 23, 2015 · 8e2cf2d · 8e2cf2d
2 parents 8ac7a90 + 0787c7e
commit 8e2cf2d
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diff --git a/openmmtools/data/src-explicit/1yi6-minimized.pdb b/openmmtools/data/src-explicit/1yi6-minimized.pdb
diff --git a/openmmtools/data/src-explicit/1yi6-pdbfixer.pdb b/openmmtools/data/src-explicit/1yi6-pdbfixer.pdb
diff --git a/openmmtools/data/src-explicit/2src-minimized.pdb b/openmmtools/data/src-explicit/2src-minimized.pdb
diff --git a/openmmtools/data/src-explicit/2src-pdbfixer.pdb b/openmmtools/data/src-explicit/2src-pdbfixer.pdb
diff --git a/openmmtools/data/src-explicit/README.md b/openmmtools/data/src-explicit/README.md
@@ -1,2 +1,2 @@
-# Src (2src) in explicit solvent
+# Src (1YI6) in explicit solvent
 This file was prepared using the accompanying `prepare_pdb.py` script
diff --git a/openmmtools/data/src-explicit/prepare_pdb.py b/openmmtools/data/src-explicit/prepare_pdb.py
@@ -18,7 +18,7 @@
 # OPTIONS
 ################################################################################
 
-pdbid = '2src' # PDB ID to retrieve
+pdbid = '1yi6' # PDB ID to retrieve
 chain_ids_to_keep = ['A'] # chains to keep
 pH = 7.0 # pH
 forcefields_to_use = ['amber99sbildn.xml', 'tip3p.xml'] # list of forcefields to use in parameterization
@@ -52,7 +52,7 @@ def write_file(filename, contents):
 all_chains = list(fixer.topology.chains())
 chain_id_list = [c.chain_id for c in fixer.structure.models[0].chains]
 chain_ids_to_remove = set(chain_id_list) - set(chain_ids_to_keep)
-fixer.removeChains(chain_ids_to_remove)
+fixer.removeChains(chainIds=chain_ids_to_remove)
 
 # Find missing residues.
 print('Finding missing residues...')

diff --git a/openmmtools/data/src-explicit/state.xml b/openmmtools/data/src-explicit/state.xml