choderalab · jchodera · Apr 10, 2015
diff --git a/examples/amber/README.md b/examples/amber/README.md
@@ -0,0 +1,5 @@
+# Examples using Amber prmtop files
+
+## Manifest
+* `hewl/` - Amber example from Amber11 for hen egg white lysozyme in implicit solvent
+* `abl-bosutinib/` - imatinib bound to the Abl kinase catalytic domain
diff --git a/examples/amber/abl-bosutinib/3UE4-pdbfixer.pdb b/examples/amber/abl-bosutinib/3UE4-pdbfixer.pdb
diff --git a/examples/amber/abl-bosutinib/3UE4.pdb b/examples/amber/abl-bosutinib/3UE4.pdb
diff --git a/examples/amber/abl-bosutinib/DB8-extract.pdb b/examples/amber/abl-bosutinib/DB8-extract.pdb
@@ -0,0 +1,37 @@
+ATOM   4358  CAA DB8 B   1      -2.439  15.823 -52.615  1.00  0.00           C  
+ATOM   4359  O02 DB8 B   1      -0.723  17.749 -43.825  1.00  0.00           O  
+ATOM   4360  CAC DB8 B   1      -0.276  10.967 -54.926  1.00  0.00           C  
+ATOM   4361  NAD DB8 B   1      -2.895  14.239 -44.070  1.00  0.00           N  
+ATOM   4362 CL1  DB8 B   1      -3.289  18.807 -42.499  1.00  0.00          Cl  
+ATOM   4363 CL2  DB8 B   1      -5.890  16.375 -46.802  1.00  0.00          Cl  
+ATOM   4364  CAG DB8 B   1      -2.532  13.891 -45.081  1.00  0.00           C  
+ATOM   4365  CAH DB8 B   1      -1.302  12.144 -46.516  1.00  0.00           C  
+ATOM   4366  CAI DB8 B   1      -4.478  17.562 -44.688  1.00  0.00           C  
+ATOM   4367  CAJ DB8 B   1      -1.826  16.646 -45.760  1.00  0.00           C  
+ATOM   4368  CAK DB8 B   1      -0.538  11.808 -50.305  1.00  0.00           C  
+ATOM   4369  CAL DB8 B   1      -2.029  14.442 -50.256  1.00  0.00           C  
+ATOM   4370  CAM DB8 B   1       0.743  10.325 -53.995  1.00  0.00           C  
+ATOM   4371  CAN DB8 B   1       0.736  11.074 -52.663  1.00  0.00           C  
+ATOM   4372  CAO DB8 B   1      -0.798   7.509 -59.039  1.00  0.00           C  
+ATOM   4373  CAP DB8 B   1      -1.308  10.319 -57.236  1.00  0.00           C  
+ATOM   4374  CAQ DB8 B   1       0.310   8.915 -56.178  1.00  0.00           C  
+ATOM   4375  CAR DB8 B   1      -0.713   9.949 -58.605  1.00  0.00           C  
+ATOM   4376  CAS DB8 B   1       0.921   8.559 -57.494  1.00  0.00           C  
+ATOM   4377  NAT DB8 B   1      -0.821  11.640 -47.769  1.00  0.00           N  
+ATOM   4378  NAU DB8 B   1      -3.037  15.528 -47.704  1.00  0.00           N  
+ATOM   4379  OAV DB8 B   1      -1.768  14.604 -52.688  1.00  0.00           O  
+ATOM   4380  OAW DB8 B   1      -0.286  12.026 -52.728  1.00  0.00           O  
+ATOM   4381  CAX DB8 B   1      -1.886  17.436 -44.492  1.00  0.00           C  
+ATOM   4382  CAY DB8 B   1      -3.217  17.893 -43.963  1.00  0.00           C  
+ATOM   4383  CAZ DB8 B   1      -4.428  16.770 -45.953  1.00  0.00           C  
+ATOM   4384  CBA DB8 B   1      -2.047  13.438 -46.419  1.00  0.00           C  
+ATOM   4385  CBB DB8 B   1      -3.098  16.314 -46.488  1.00  0.00           C  
+ATOM   4386  CBC DB8 B   1      -1.523  13.877 -51.545  1.00  0.00           C  
+ATOM   4387  CBD DB8 B   1      -0.780  12.583 -51.556  1.00  0.00           C  
+ATOM   4388  CBE DB8 B   1      -2.323  14.244 -47.677  1.00  0.00           C  
+ATOM   4389  CBF DB8 B   1      -1.045  12.359 -48.992  1.00  0.00           C  
+ATOM   4390  CBG DB8 B   1      -1.792  13.677 -48.989  1.00  0.00           C  
+ATOM   4391  NBH DB8 B   1      -0.243  10.244 -56.237  1.00  0.00           N  
+ATOM   4392  NBI DB8 B   1      -0.079   8.660 -58.514  1.00  0.00           N  
+ATOM   4393  C01 DB8 B   1       0.358  16.878 -43.861  1.00  0.00           C  
+TER    4394      DB8 B   1
diff --git a/examples/amber/abl-bosutinib/README.md b/examples/amber/abl-bosutinib/README.md
@@ -0,0 +1,7 @@
+# Imatinib binding to Abl kinase catalytic domain
+
+## Manifest
+
+* `3UE4.pdb` - Original PDB file for Abl kinase catalytic domain with imatinib
+* `3UE4-pdbfixer.pdb` - Abl kinase (with heavy atoms and hydrogen added) complexed with bosutinib (DB8) containing only heavy atoms
+* `DB8-extract.pdb` - bosutinib (DB8) extracted from `3UE4-pdbfixer.pdb`, only heavy atoms from X-ray structure
diff --git a/amber-example/README.md → examples/amber/hewl/README.md b/amber-example/README.md → examples/amber/hewl/README.md
diff --git a/amber-example/Run.cnstph → examples/amber/hewl/Run.cnstph b/amber-example/Run.cnstph → examples/amber/hewl/Run.cnstph
diff --git a/amber-example/cpin → examples/amber/hewl/cpin b/amber-example/cpin → examples/amber/hewl/cpin
diff --git a/amber-example/cpout.save → examples/amber/hewl/cpout.save b/amber-example/cpout.save → examples/amber/hewl/cpout.save
diff --git a/amber-example/cpr → examples/amber/hewl/cpr b/amber-example/cpr → examples/amber/hewl/cpr
diff --git a/amber-example/example.pdb → examples/amber/hewl/example.pdb b/amber-example/example.pdb → examples/amber/hewl/example.pdb
diff --git a/amber-example/mdout.save → examples/amber/hewl/mdout.save b/amber-example/mdout.save → examples/amber/hewl/mdout.save
diff --git a/amber-example/min.x → examples/amber/hewl/min.x b/amber-example/min.x → examples/amber/hewl/min.x
diff --git a/amber-example/prmcrd → examples/amber/hewl/prmcrd b/amber-example/prmcrd → examples/amber/hewl/prmcrd
diff --git a/amber-example/prmtop → examples/amber/hewl/prmtop b/amber-example/prmtop → examples/amber/hewl/prmtop