Tue Oct 11 00:56:36 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 00:56:36 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: LEU 299 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6423790 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -15.23900 33.15100 ymin,ymax (A): -25.97700 27.49900 zmin,zma (A): -22.98400 32.43500 x,y,z range (A): 48.39000 53.47600 55.41900 scale (grids/A): 0.6423790 object centre (A): 8.956001 0.7610006 4.725499 number of atom coordinates read : 2764 total number of charged atoms : 2612 net assigned charge : 6.040016 assigned positive charge : 418.5976 centred at (gu) : 89.27554 89.07836 89.91722 assigned negative charge : -412.5582 centred at (gu) : 89.27463 89.09159 90.22823 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7574 nv = 96 ne = 84 npr = 56028 no. pairs analyzed = 56028 no. exposed pairs = 3276 no. arc points = 23333 no. surface atoms = 1110 nbur = 1654 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 383 mr = 4271 m= 4 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 105 time to turn everything in is 0.3700000 number of dielectric boundary points 3639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2159 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9109 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0040413E-08 -3.2502403E-08 midg,1,midg; midg,igrid,midg 1.3532667E-08 6.3650232E-09 1,midg,midg; igrid,midg,midg 1.0797611E-08 8.2222895E-09 gauss-seidel spectral radius is 0.9874564 estimated iterations to convergence 73 setup time was (sec) 0.6400000 now iterating at: 00:56:37 rms-change max change #iterations 0.1589333 21.83330 at 10iterations 1.6149670E-02 2.216048 at 20iterations 1.8602178E-03 0.3059425 at 30iterations 3.2917361E-04 6.4308167E-02 at 40iterations 7.5866279E-05 1.7475128E-02 at 50iterations finished qdiffx linear iterations at : 00:56:40 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 7.5866279E-05 1.7475128E-02 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 00:56:41 4.159u 0.282s 0:05.07 87.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 00:56:41 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: LEU 299 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.927137 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -15.23900 33.15100 ymin,ymax (A): -25.97700 27.49900 zmin,zma (A): -22.98400 32.43500 x,y,z range (A): 48.39000 53.47600 55.41900 scale (grids/A): 1.927137 object centre (A): 8.956001 0.7610006 4.725499 number of atom coordinates read : 2764 total number of charged atoms : 2612 net assigned charge : 6.040016 assigned positive charge : 418.5976 centred at (gu) : 87.82625 87.23482 89.75094 assigned negative charge : -412.5582 centred at (gu) : 87.82362 87.27423 90.68436 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 82414 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23333 grid for indexing accessible points = 1.400000 m= 29469 mr = 57883 m= 4581 mr = 22107 m= 258 mr = 2992 m= 2 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 3961 time to turn everything in is 0.7200000 number of dielectric boundary points 33623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20569 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6423790 object centre at (A) : 8.956001 0.7610006 4.725499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9931540E-02 -4.2711593E-02 midg,1,midg; midg,igrid,midg 6.8577018E-04 2.3241756E-02 1,midg,midg; igrid,midg,midg 1.4153043E-02 8.1150141E-03 gauss-seidel spectral radius is 0.9986781 estimated iterations to convergence 218 setup time was (sec) 1.030000 now iterating at: 00:56:43 rms-change max change #iterations 4.563549 173.9639 at 10iterations 2.155915 70.49820 at 20iterations 1.023286 33.61524 at 30iterations 0.4850556 14.97304 at 40iterations 0.2298952 7.520180 at 50iterations 0.1087197 3.234245 at 60iterations 5.1849864E-02 1.614632 at 70iterations 2.4636902E-02 0.6967888 at 80iterations 1.1744344E-02 0.3477802 at 90iterations 5.6530265E-03 0.1627808 at 100iterations 2.7543900E-03 8.5632324E-02 at 110iterations 1.3702600E-03 4.4822693E-02 at 120iterations finished qdiffx linear iterations at : 00:56:51 total time elapsed so far: 9.580000 # loops : 120 mean,max change (kT/e) : 1.3702600E-03 4.4822693E-02 energy calculations done at 9.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.750000 DelPhi exited at 00:56:52 9.757u 0.310s 0:10.65 94.4% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 00:56:52 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: LEU 299 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.890705 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -15.23900 33.15100 ymin,ymax (A): -25.97700 27.49900 zmin,zma (A): -22.98400 32.43500 x,y,z range (A): 48.39000 53.47600 55.41900 scale (grids/A): 2.890705 object centre (A): 8.956001 0.7610006 4.725499 number of atom coordinates read : 2764 total number of charged atoms : 2612 net assigned charge : 6.040016 assigned positive charge : 418.5976 centred at (gu) : 86.73933 85.85197 89.62625 assigned negative charge : -412.5582 centred at (gu) : 86.73522 85.91127 91.02647 start vw surface at 0.1700000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 190399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23333 grid for indexing accessible points = 1.400000 m= 96283 mr = 139785 m= 34359 mr = 79625 m= 8259 mr = 28035 m= 1266 mr = 6368 m= 71 mr = 906 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 12949 time to turn everything in is 1.870000 number of dielectric boundary points 75871 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 20895 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.927137 object centre at (A) : 8.956001 0.7610006 4.725499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9254968 -0.4563495 midg,1,midg; midg,igrid,midg -4.6845052E-02 0.1649721 1,midg,midg; igrid,midg,midg 0.3281668 9.6715197E-02 gauss-seidel spectral radius is 0.9992643 estimated iterations to convergence 291 setup time was (sec) 2.200000 now iterating at: 00:56:54 rms-change max change #iterations 10.45330 442.5620 at 10iterations 6.090211 201.0080 at 20iterations 3.544551 103.6171 at 30iterations 2.052746 45.81205 at 40iterations 1.185731 33.82125 at 50iterations 0.6849566 12.65256 at 60iterations 0.3952379 8.812531 at 70iterations 0.2277701 4.013855 at 80iterations 0.1310525 2.592455 at 90iterations 7.5713880E-02 1.327858 at 100iterations 4.3743331E-02 0.8330765 at 110iterations 2.5185680E-02 0.4386253 at 120iterations 1.4545823E-02 0.2888985 at 130iterations 8.4321080E-03 0.1465893 at 140iterations 4.9092667E-03 9.3608856E-02 at 150iterations 2.8910108E-03 5.2860260E-02 at 160iterations 1.7387737E-03 3.5076141E-02 at 170iterations 1.0808989E-03 2.5703430E-02 at 180iterations finished qdiffx linear iterations at : 00:57:09 total time elapsed so far: 16.44000 # loops : 180 mean,max change (kT/e) : 1.0808989E-03 2.5703430E-02 energy calculations done at 16.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.62000 DelPhi exited at 00:57:09 16.623u 0.310s 0:17.48 96.8% 0+0k 0+0io 0pf+0w