Tue Oct 11 05:17:34 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 05:17:34 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2243 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: ZN7 739 has a net charge of 1.4000 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: 0.6913561 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): 19.71900 63.10400 ymin,ymax (A): -3.539000 33.55700 zmin,zma (A): 20.28900 71.78201 x,y,z range (A): 43.38500 37.09600 51.49300 scale (grids/A): 0.6913561 object centre (A): 41.41150 15.00900 46.03550 number of atom coordinates read : 2243 total number of charged atoms : 1932 net assigned charge : 8.031008 assigned positive charge : 313.3770 centred at (gu) : 90.17316 89.66980 89.35512 assigned negative charge : -305.3461 centred at (gu) : 90.34272 89.66862 89.32248 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6743 nv = 96 ne = 84 npr = 40847 no. pairs analyzed = 40847 no. exposed pairs = 2514 no. arc points = 17050 no. surface atoms = 864 nbur = 1379 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3855 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3232 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1725 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7586 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9756042E-08 5.0374641E-08 midg,1,midg; midg,igrid,midg 4.8776325E-08 4.3705690E-08 1,midg,midg; igrid,midg,midg 9.8586241E-08 -1.2174545E-08 gauss-seidel spectral radius is 0.9890965 estimated iterations to convergence 78 setup time was (sec) 0.4700000 now iterating at: 05:17:35 rms-change max change #iterations 0.1770337 24.32758 at 10iterations 2.1416409E-02 2.797110 at 20iterations 2.5899741E-03 0.3176045 at 30iterations 3.6833825E-04 5.1292419E-02 at 40iterations 7.4649004E-05 9.1285706E-03 at 50iterations finished qdiffx linear iterations at : 05:17:37 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 7.4649004E-05 9.1285706E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 05:17:38 3.240u 0.197s 0:03.99 85.9% 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 05:17:38 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2243 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: ZN7 739 has a net charge of 1.4000 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: 2.074068 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): 19.71900 63.10400 ymin,ymax (A): -3.539000 33.55700 zmin,zma (A): 20.28900 71.78201 x,y,z range (A): 43.38500 37.09600 51.49300 scale (grids/A): 2.074068 object centre (A): 41.41150 15.00900 46.03550 number of atom coordinates read : 2243 total number of charged atoms : 1932 net assigned charge : 8.031008 assigned positive charge : 313.3770 centred at (gu) : 90.51951 89.00956 88.06506 assigned negative charge : -305.3461 centred at (gu) : 91.02810 89.00597 87.96755 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 71307 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17050 grid for indexing accessible points = 1.400000 m= 28711 mr = 50561 m= 5322 mr = 21749 m= 410 mr = 3532 m= 6 mr = 189 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 29725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 15332 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) : 0.6913561 object centre at (A) : 41.41150 15.00900 46.03550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9085099E-02 4.6265285E-02 midg,1,midg; midg,igrid,midg 2.2158187E-02 2.0959048E-02 1,midg,midg; igrid,midg,midg 4.0060956E-02 1.0023060E-02 gauss-seidel spectral radius is 0.9987803 estimated iterations to convergence 227 setup time was (sec) 0.8500000 now iterating at: 05:17:39 rms-change max change #iterations 4.417986 203.7113 at 10iterations 2.163916 78.40660 at 20iterations 1.052481 33.27534 at 30iterations 0.5168669 17.64017 at 40iterations 0.2523186 8.160864 at 50iterations 0.1236194 4.508882 at 60iterations 6.0583983E-02 1.810593 at 70iterations 2.9650260E-02 0.8624649 at 80iterations 1.4484419E-02 0.4431067 at 90iterations 7.1366956E-03 0.2213287 at 100iterations 3.5114817E-03 0.1158676 at 110iterations 1.7467445E-03 4.9669266E-02 at 120iterations finished qdiffx linear iterations at : 05:17:45 total time elapsed so far: 7.180000 # loops : 120 mean,max change (kT/e) : 1.7467445E-03 4.9669266E-02 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.390000 DelPhi exited at 05:17:46 7.392u 0.234s 0:07.99 95.3% 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 05:17:46 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2243 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: ZN7 739 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 3.111102 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): 19.71900 63.10400 ymin,ymax (A): -3.539000 33.55700 zmin,zma (A): 20.28900 71.78201 x,y,z range (A): 43.38500 37.09600 51.49300 scale (grids/A): 3.111102 object centre (A): 41.41150 15.00900 46.03550 number of atom coordinates read : 2243 total number of charged atoms : 1932 net assigned charge : 8.031008 assigned positive charge : 313.3770 centred at (gu) : 90.77924 88.51425 87.09765 assigned negative charge : -305.3461 centred at (gu) : 91.54226 88.50890 86.95130 start vw surface at 0.2100000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 164508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17050 grid for indexing accessible points = 1.400000 m= 89727 mr = 121975 m= 36158 mr = 74624 m= 10011 mr = 29631 m= 1836 mr = 7681 m= 154 mr = 1345 m= 2 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.670000 number of dielectric boundary points 67057 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 15456 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) : 2.074068 object centre at (A) : 41.41150 15.00900 46.03550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3798776 0.3457849 midg,1,midg; midg,igrid,midg 0.1950491 0.1869569 1,midg,midg; igrid,midg,midg 0.3273290 0.2607674 gauss-seidel spectral radius is 0.9992820 estimated iterations to convergence 294 setup time was (sec) 1.950000 now iterating at: 05:17:48 rms-change max change #iterations 9.903614 331.6104 at 10iterations 5.856019 155.6341 at 20iterations 3.450258 73.92075 at 30iterations 2.023427 41.73915 at 40iterations 1.186689 25.29826 at 50iterations 0.6943891 16.72692 at 60iterations 0.4055828 7.781705 at 70iterations 0.2371343 4.986809 at 80iterations 0.1383943 2.593495 at 90iterations 8.0598868E-02 1.659487 at 100iterations 4.7080334E-02 0.9110413 at 110iterations 2.7522067E-02 0.5359921 at 120iterations 1.6149521E-02 0.3028030 at 130iterations 9.5543060E-03 0.1740494 at 140iterations 5.7455883E-03 0.1092091 at 150iterations 3.5187998E-03 6.6352844E-02 at 160iterations 2.2551962E-03 4.7523499E-02 at 170iterations 1.5187528E-03 3.3491135E-02 at 180iterations finished qdiffx linear iterations at : 05:17:58 total time elapsed so far: 11.38000 # loops : 180 mean,max change (kT/e) : 1.5187528E-03 3.3491135E-02 energy calculations done at 11.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 05:17:58 11.562u 0.185s 0:12.31 95.3% 0+0k 0+0io 0pf+0w