Sun Oct 9 16:04:24 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 Sun Oct 9 2011 at 16:04:24 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3114 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: GLM 240 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6301332 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): -15.24200 37.22100 ymin,ymax (A): 55.58300 108.5770 zmin,zma (A): -5.276000 51.22000 x,y,z range (A): 52.46300 52.99400 56.49600 scale (grids/A): 0.6301332 object centre (A): 10.98950 82.08000 22.97200 number of atom coordinates read : 3114 total number of charged atoms : 2961 net assigned charge : -3.687976 assigned positive charge : 461.8041 centred at (gu) : 90.17410 88.44105 91.27027 assigned negative charge : -465.4935 centred at (gu) : 90.20322 88.34388 91.33039 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8022 nv = 96 ne = 84 npr = 64865 no. pairs analyzed = 64865 no. exposed pairs = 3785 no. arc points = 26362 no. surface atoms = 1292 nbur = 1822 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 459 mr = 4360 m= 0 mr = 60 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3900000 number of dielectric boundary points 4061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2582 ## 269 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9992 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9246467E-09 -1.3381083E-08 midg,1,midg; midg,igrid,midg -1.9923467E-08 4.5401749E-09 1,midg,midg; igrid,midg,midg -6.3284461E-10 -7.0811677E-09 gauss-seidel spectral radius is 0.9869969 estimated iterations to convergence 72 setup time was (sec) 0.6100000 now iterating at: 16:04:25 rms-change max change #iterations 0.1542913 22.29984 at 10iterations 1.4751766E-02 1.940399 at 20iterations 1.4133607E-03 0.1777229 at 30iterations 1.3642927E-04 1.5621185E-02 at 40iterations 1.3623339E-05 1.6460419E-03 at 50iterations finished qdiffx linear iterations at : 16:04:27 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.3623339E-05 1.6460419E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 16:04:28 3.460u 0.160s 0:03.96 91.4% 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 Sun Oct 9 2011 at 16:04:28 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3114 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: GLM 240 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.890399 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): -15.24200 37.22100 ymin,ymax (A): 55.58300 108.5770 zmin,zma (A): -5.276000 51.22000 x,y,z range (A): 52.46300 52.99400 56.49600 scale (grids/A): 1.890399 object centre (A): 10.98950 82.08000 22.97200 number of atom coordinates read : 3114 total number of charged atoms : 2961 net assigned charge : -3.687976 assigned positive charge : 461.8041 centred at (gu) : 90.52153 85.32246 93.81012 assigned negative charge : -465.4935 centred at (gu) : 90.60948 85.03153 93.99111 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 87009 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26362 grid for indexing accessible points = 1.400000 m= 31168 mr = 60574 m= 5341 mr = 22423 m= 322 mr = 3228 m= 2 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 37504 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 23273 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) : 0.6301332 object centre at (A) : 10.98950 82.08000 22.97200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7543815E-02 9.8484810E-03 midg,1,midg; midg,igrid,midg -1.9696422E-02 -7.4978243E-03 1,midg,midg; igrid,midg,midg -3.4362573E-02 -3.3836767E-02 gauss-seidel spectral radius is 0.9986580 estimated iterations to convergence 216 setup time was (sec) 0.9300000 now iterating at: 16:04:29 rms-change max change #iterations 4.653959 193.3030 at 10iterations 2.183332 78.74873 at 20iterations 1.026843 35.31271 at 30iterations 0.4824507 13.24366 at 40iterations 0.2278858 6.683195 at 50iterations 0.1073388 3.219895 at 60iterations 5.0537106E-02 1.523328 at 70iterations 2.3875115E-02 0.7114658 at 80iterations 1.1226901E-02 0.3475399 at 90iterations 5.2984264E-03 0.1513042 at 100iterations 2.5049404E-03 7.4100494E-02 at 110iterations 1.1836771E-03 3.3691406E-02 at 120iterations finished qdiffx linear iterations at : 16:04:35 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 1.1836771E-03 3.3691406E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 16:04:36 7.666u 0.180s 0:08.19 95.7% 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 Sun Oct 9 2011 at 16:04:36 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3114 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: GLM 240 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.835599 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): -15.24200 37.22100 ymin,ymax (A): 55.58300 108.5770 zmin,zma (A): -5.276000 51.22000 x,y,z range (A): 52.46300 52.99400 56.49600 scale (grids/A): 2.835599 object centre (A): 10.98950 82.08000 22.97200 number of atom coordinates read : 3114 total number of charged atoms : 2961 net assigned charge : -3.687976 assigned positive charge : 461.8041 centred at (gu) : 90.78207 82.98347 95.71500 assigned negative charge : -465.4935 centred at (gu) : 90.91409 82.54709 95.98662 start vw surface at 0.1600000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 201407 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26362 grid for indexing accessible points = 1.400000 m= 99787 mr = 146893 m= 37159 mr = 80504 m= 9604 mr = 29272 m= 1420 mr = 7064 m= 89 mr = 917 m= 0 mr = 26 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.670000 number of dielectric boundary points 84790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 23687 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) : 1.890399 object centre at (A) : 10.98950 82.08000 22.97200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4832088 0.2413310 midg,1,midg; midg,igrid,midg -0.2074880 -0.2417733 1,midg,midg; igrid,midg,midg -0.4067581 -0.3628237 gauss-seidel spectral radius is 0.9992730 estimated iterations to convergence 293 setup time was (sec) 1.980000 now iterating at: 16:04:38 rms-change max change #iterations 10.97186 374.6949 at 10iterations 6.469716 132.1807 at 20iterations 3.799743 69.15597 at 30iterations 2.225207 40.64754 at 40iterations 1.295480 23.86296 at 50iterations 0.7548023 13.89581 at 60iterations 0.4384735 7.480286 at 70iterations 0.2543936 4.858606 at 80iterations 0.1478980 2.529099 at 90iterations 8.5623942E-02 1.508476 at 100iterations 4.9557094E-02 0.9366555 at 110iterations 2.8684638E-02 0.5672488 at 120iterations 1.6634928E-02 0.2761588 at 130iterations 9.6192677E-03 0.1631508 at 140iterations 5.5816323E-03 9.0717316E-02 at 150iterations 3.2452620E-03 6.2331200E-02 at 160iterations 1.8836590E-03 3.1898499E-02 at 170iterations 1.1070957E-03 2.0828247E-02 at 180iterations finished qdiffx linear iterations at : 16:04:49 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 1.1070957E-03 2.0828247E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 16:04:49 12.596u 0.165s 0:13.03 97.8% 0+0k 0+0io 0pf+0w