Merge pull request #406 from swails/master

Add support for native CHARMM files

examples/ala_ala_ala.pdb

+REMARK *                                                                              
+REMARK   DATE:     8/ 5/ 9     14:44:19      CREATED BY USER: mjw                     
+ATOM      1  N   ALA     1       0.024  -0.103  -0.101  1.00  0.00      AAL 
+ATOM      2  HT1 ALA     1       0.027  -1.132  -0.239  1.00  0.00      AAL 
+ATOM      3  HT2 ALA     1      -0.805   0.163   0.471  1.00  0.00      AAL 
+ATOM      4  HT3 ALA     1      -0.059   0.384  -1.019  1.00  0.00      AAL 
+ATOM      5  CA  ALA     1       1.247   0.375   0.636  1.00  0.00      AAL 
+ATOM      6  HA  ALA     1       0.814   0.861   1.495  1.00  0.00      AAL 
+ATOM      7  CB  ALA     1       2.057  -0.772   1.289  1.00  0.00      AAL 
+ATOM      8  HB1 ALA     1       3.136  -0.752   1.032  1.00  0.00      AAL 
+ATOM      9  HB2 ALA     1       1.990  -0.641   2.395  1.00  0.00      AAL 
+ATOM     10  HB3 ALA     1       1.656  -1.782   1.063  1.00  0.00      AAL 
+ATOM     11  C   ALA     1       1.956   1.579   0.036  1.00  0.00      AAL 
+ATOM     12  O   ALA     1       1.219   2.525  -0.201  1.00  0.00      AAL 
+ATOM     13  N   ALA     2       3.289   1.631  -0.202  1.00  0.00      AAL 
+ATOM     14  HN  ALA     2       3.939   0.868  -0.174  1.00  0.00      AAL 
+ATOM     15  CA  ALA     2       3.990   2.909  -0.215  1.00  0.00      AAL 
+ATOM     16  HA  ALA     2       3.742   3.440   0.695  1.00  0.00      AAL 
+ATOM     17  CB  ALA     2       3.662   3.802  -1.434  1.00  0.00      AAL 
+ATOM     18  HB1 ALA     2       4.192   4.778  -1.358  1.00  0.00      AAL 
+ATOM     19  HB2 ALA     2       3.956   3.311  -2.382  1.00  0.00      AAL 
+ATOM     20  HB3 ALA     2       2.577   4.027  -1.467  1.00  0.00      AAL 
+ATOM     21  C   ALA     2       5.487   2.654  -0.128  1.00  0.00      AAL 
+ATOM     22  O   ALA     2       5.889   1.489  -0.137  1.00  0.00      AAL 
+ATOM     23  N   ALA     3       6.275   3.733  -0.037  1.00  0.00      AAL 
+ATOM     24  HN  ALA     3       5.963   4.691  -0.028  1.00  0.00      AAL 
+ATOM     25  CA  ALA     3       7.707   3.802   0.068  1.00  0.00      AAL 
+ATOM     26  HA  ALA     3       8.160   3.418  -0.833  1.00  0.00      AAL 
+ATOM     27  CB  ALA     3       8.233   3.093   1.333  1.00  0.00      AAL 
+ATOM     28  HB1 ALA     3       9.342   3.149   1.356  1.00  0.00      AAL 
+ATOM     29  HB2 ALA     3       7.835   3.593   2.240  1.00  0.00      AAL 
+ATOM     30  HB3 ALA     3       7.923   2.030   1.332  1.00  0.00      AAL 
+ATOM     31  C   ALA     3       8.018   5.323   0.136  1.00  0.00      AAL 
+ATOM     32  OT1 ALA     3       7.032   6.119   0.127  1.00  0.00      AAL 
+ATOM     33  OT2 ALA     3       9.219   5.692   0.188  1.00  0.00      AAL 
+TER      34      ALA      3
+END

examples/ala_ala_ala.psf

+PSF CMAP CHEQ
+
+       2 !NTITLE
+**                                                                              
+*  DATE:     8/ 5/ 9     14:44:19      CREATED BY USER: mjw                     
+
+      33 !NATOM
+       1 AAL  1    ALA  N      56  -0.300000       14.0070           0   0.00000     -0.301140E-02
+       2 AAL  1    ALA  HT1     2   0.330000       1.00800           0   0.00000     -0.301140E-02
+       3 AAL  1    ALA  HT2     2   0.330000       1.00800           0   0.00000     -0.301140E-02
+       4 AAL  1    ALA  HT3     2   0.330000       1.00800           0   0.00000     -0.301140E-02
+       5 AAL  1    ALA  CA     22   0.210000       12.0110           0   0.00000     -0.301140E-02
+       6 AAL  1    ALA  HA      6   0.100000       1.00800           0   0.00000     -0.301140E-02
+       7 AAL  1    ALA  CB     24  -0.270000       12.0110           0   0.00000     -0.301140E-02
+       8 AAL  1    ALA  HB1     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02
+       9 AAL  1    ALA  HB2     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02
+      10 AAL  1    ALA  HB3     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02
+      11 AAL  1    ALA  C      20   0.510000       12.0110           0   0.00000     -0.301140E-02
+      12 AAL  1    ALA  O      70  -0.510000       15.9990           0   0.00000     -0.301140E-02
+      13 AAL  2    ALA  N      54  -0.470000       14.0070           0   0.00000     -0.301140E-02
+      14 AAL  2    ALA  HN      1   0.310000       1.00800           0   0.00000     -0.301140E-02
+      15 AAL  2    ALA  CA     22   0.700000E-01   12.0110           0   0.00000     -0.301140E-02
+      16 AAL  2    ALA  HA      6   0.900000E-01   1.00800           0   0.00000     -0.301140E-02
+      17 AAL  2    ALA  CB     24  -0.270000       12.0110           0   0.00000     -0.301140E-02
+      18 AAL  2    ALA  HB1     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02
+      19 AAL  2    ALA  HB2     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02
+      20 AAL  2    ALA  HB3     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02
+      21 AAL  2    ALA  C      20   0.510000       12.0110           0   0.00000     -0.301140E-02
+      22 AAL  2    ALA  O      70  -0.510000       15.9990           0   0.00000     -0.301140E-02
+      23 AAL  3    ALA  N      54  -0.470000       14.0070           0   0.00000     -0.301140E-02
+      24 AAL  3    ALA  HN      1   0.310000       1.00800           0   0.00000     -0.301140E-02
+      25 AAL  3    ALA  CA     22   0.700000E-01   12.0110           0   0.00000     -0.301140E-02
+      26 AAL  3    ALA  HA      6   0.900000E-01   1.00800           0   0.00000     -0.301140E-02
+      27 AAL  3    ALA  CB     24  -0.270000       12.0110           0   0.00000     -0.301140E-02
+      28 AAL  3    ALA  HB1     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02
+      29 AAL  3    ALA  HB2     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02
+      30 AAL  3    ALA  HB3     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02
+      31 AAL  3    ALA  C      32   0.340000       12.0110           0   0.00000     -0.301140E-02
+      32 AAL  3    ALA  OT1    72  -0.670000       15.9990           0   0.00000     -0.301140E-02
+      33 AAL  3    ALA  OT2    72  -0.670000       15.9990           0   0.00000     -0.301140E-02
+
+      32 !NBOND: bonds
+       2       1       3       1       4       1       7       5
+       1       5      11       5      11      13       5       6
+       7       8       7       9       7      10      12      11
+      17      15      13      14      13      15      21      15
+      21      23      15      16      17      18      17      19
+      17      20      22      21      27      25      23      24
+      23      25      31      25      25      26      27      28
+      27      29      27      30      31      33      31      32
+
+      57 !NTHETA: angles
+       2       1       3       2       1       4       2       1       5
+       3       1       4       3       1       5       4       1       5
+       1       5       6       1       5       7       1       5      11
+       6       5       7       6       5      11       7       5      11
+       5       7       8       5       7       9       5       7      10
+       8       7       9       8       7      10       9       7      10
+       5      11      12       5      11      13      12      11      13
+      11      13      14      11      13      15      14      13      15
+      13      15      16      13      15      17      13      15      21
+      16      15      17      16      15      21      17      15      21
+      15      17      18      15      17      19      15      17      20
+      18      17      19      18      17      20      19      17      20
+      15      21      22      15      21      23      22      21      23
+      21      23      24      21      23      25      24      23      25
+      23      25      26      23      25      27      23      25      31
+      26      25      27      26      25      31      27      25      31
+      25      27      28      25      27      29      25      27      30
+      28      27      29      28      27      30      29      27      30
+      25      31      32      25      31      33      32      31      33
+
+      74 !NPHI: dihedrals
+       1       5       7       8       1       5       7       9
+       1       5       7      10       1       5      11      12
+       1       5      11      13       2       1       5       6
+       2       1       5       7       2       1       5      11
+       3       1       5       6       3       1       5       7
+       3       1       5      11       4       1       5       6
+       4       1       5       7       4       1       5      11
+       5      11      13      14       5      11      13      15
+       6       5       7       8       6       5       7       9
+       6       5       7      10       6       5      11      12
+       6       5      11      13       7       5      11      12
+       7       5      11      13       8       7       5      11
+       9       7       5      11      10       7       5      11
+      11      13      15      16      11      13      15      17
+      11      13      15      21      12      11      13      14
+      12      11      13      15      13      15      17      18
+      13      15      17      19      13      15      17      20
+      13      15      21      22      13      15      21      23
+      14      13      15      16      14      13      15      17
+      14      13      15      21      15      21      23      24
+      15      21      23      25      16      15      17      18
+      16      15      17      19      16      15      17      20
+      16      15      21      22      16      15      21      23
+      17      15      21      22      17      15      21      23
+      18      17      15      21      19      17      15      21
+      20      17      15      21      21      23      25      26
+      21      23      25      27      21      23      25      31
+      22      21      23      24      22      21      23      25
+      23      25      27      28      23      25      27      29
+      23      25      27      30      23      25      31      32
+      23      25      31      33      24      23      25      26
+      24      23      25      27      24      23      25      31
+      26      25      27      28      26      25      27      29
+      26      25      27      30      26      25      31      32
+      26      25      31      33      27      25      31      32
+      27      25      31      33      28      27      25      31
+      29      27      25      31      30      27      25      31
+
+       5 !NIMPHI: impropers
+      11       5      13      12      13      11      15      14
+      21      15      23      22      23      21      25      24
+      31      25      33      32
+
+       5 !NDON: donors
+       1       2       1       3       1       4      13      14
+      23      24
+
+       4 !NACC: acceptors
+      12      11      22      21      32      31      33      31
+
+       0 !NNB
+
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0
+
+       9       0 !NGRP NST2
+       0       2       0       6       1       0      10       1       0
+      12       1       0      16       1       0      20       1       0
+      22       1       0      26       1       0      30       2       0
+
+       1 !MOLNT
+       1       1       1       1       1       1       1       1
+       1       1       1       1       1       1       1       1
+       1       1       1       1       1       1       1       1
+       1       1       1       1       1       1       1       1
+       1
+
+       0       0 !NUMLP NUMLPH
+
+       1 !NCRTERM: cross-terms
+      11      13      15      21      13      15      21      23

examples/simulateCharmm.py

+from simtk.openmm.app import *
+from simtk.openmm import *
+from simtk.unit import *
+from sys import stdout, exit, stderr
+
+# Read the PSF
+psf = CharmmPsfFile('ala_ala_ala.psf')
+
+# Get the coordinates from the PDB
+pdb = PDBFile('ala_ala_ala.pdb')
+
+# Load the parameter set.
+params = CharmmParameterSet('charmm22.rtf', 'charmm22.par')
+
+# NOTICE:
+# -------
+# The CHARMM 22 parameter set is out-of-date and NOT recommended for general
+# use. It is included here as an illustrative example, but for production
+# simulations you should download the latest versions of the force fields at
+# http://mackerell.umaryland.edu/CHARMM_ff_params.html
+
+# Instantiate the system
+system = psf.createSystem(params, nonbondedMethod=NoCutoff,
+                          nonbondedCutoff=None)
+integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
+simulation = Simulation(psf.topology, system, integrator)
+simulation.context.setPositions(pdb.getPositions())
+simulation.minimizeEnergy()
+simulation.reporters.append(PDBReporter('ch_output.pdb', 1000))
+simulation.reporters.append(
+        StateDataReporter(stdout, 1000, step=True, potentialEnergy=True,
+                          temperature=True)
+)
+simulation.step(10000)