Tue Oct 11 06:02:49 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+sph.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 = amb.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 06:02:49 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 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: 0.7045877 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): 25.72000 72.08800 ymin,ymax (A): -18.93400 31.59200 zmin,zma (A): 4.023000 46.35600 x,y,z range (A): 46.36800 50.52600 42.33300 scale (grids/A): 0.7045877 object centre (A): 48.90400 6.329000 25.18950 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 89.27194 90.21951 90.33261 assigned negative charge : -318.8441 centred at (gu) : 89.40034 90.16985 90.41933 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7185 nv = 96 ne = 84 npr = 42746 no. pairs analyzed = 42746 no. exposed pairs = 2624 no. arc points = 17673 no. surface atoms = 898 nbur = 1429 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 4144 m= 2 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3435 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1638 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7978 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5940194E-08 9.8672199E-09 midg,1,midg; midg,igrid,midg 2.6198208E-08 7.7530849E-08 1,midg,midg; igrid,midg,midg 1.2799309E-07 -8.9112415E-09 gauss-seidel spectral radius is 0.9895038 estimated iterations to convergence 79 setup time was (sec) 0.5100000 now iterating at: 06:02:50 rms-change max change #iterations 0.1983531 34.36520 at 10iterations 2.4747066E-02 2.952595 at 20iterations 3.3397749E-03 0.4604378 at 30iterations 6.1010674E-04 7.4695587E-02 at 40iterations 1.6934940E-04 1.7883301E-02 at 50iterations finished qdiffx linear iterations at : 06:02:53 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.6934940E-04 1.7883301E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 06:02:53 3.353u 0.207s 0:03.91 90.7% 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 Tue Oct 11 2011 at 06:02:53 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 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: 2.113763 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): 25.72000 72.08800 ymin,ymax (A): -18.93400 31.59200 zmin,zma (A): 4.023000 46.35600 x,y,z range (A): 46.36800 50.52600 42.33300 scale (grids/A): 2.113763 object centre (A): 48.90400 6.329000 25.18950 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 87.81605 90.65853 90.99773 assigned negative charge : -318.8441 centred at (gu) : 88.20112 90.50953 91.25812 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75966 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17673 grid for indexing accessible points = 1.400000 m= 30855 mr = 54217 m= 5849 mr = 23410 m= 478 mr = 3879 m= 23 mr = 215 m= 0 mr = 4 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 31446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 15869 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) : 0.7045877 object centre at (A) : 48.90400 6.329000 25.18950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0632392E-02 2.6700012E-02 midg,1,midg; midg,igrid,midg 4.7338836E-02 2.7824549E-02 1,midg,midg; igrid,midg,midg 4.3159772E-02 -4.4261824E-02 gauss-seidel spectral radius is 0.9988262 estimated iterations to convergence 231 setup time was (sec) 0.8600000 now iterating at: 06:02:54 rms-change max change #iterations 4.618311 167.8973 at 10iterations 2.278967 73.31812 at 20iterations 1.130094 35.65299 at 30iterations 0.5599687 16.08768 at 40iterations 0.2774999 8.731613 at 50iterations 0.1376096 4.048092 at 60iterations 6.8265229E-02 2.171906 at 70iterations 3.3960022E-02 0.9881248 at 80iterations 1.6981941E-02 0.5110130 at 90iterations 8.5392939E-03 0.2520416 at 100iterations 4.3173255E-03 0.1312485 at 110iterations 2.2602696E-03 6.6083908E-02 at 120iterations finished qdiffx linear iterations at : 06:03:01 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 2.2602696E-03 6.6083908E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 06:03:01 7.517u 0.240s 0:08.19 94.6% 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 06:03:01 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 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: 3.170645 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): 25.72000 72.08800 ymin,ymax (A): -18.93400 31.59200 zmin,zma (A): 4.023000 46.35600 x,y,z range (A): 46.36800 50.52600 42.33300 scale (grids/A): 3.170645 object centre (A): 48.90400 6.329000 25.18950 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 86.72395 90.98772 91.49664 assigned negative charge : -318.8441 centred at (gu) : 87.30168 90.76434 91.88722 start vw surface at 0.1500000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 175159 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17673 grid for indexing accessible points = 1.400000 m= 96087 mr = 130589 m= 38840 mr = 79888 m= 10913 mr = 31931 m= 2025 mr = 8457 m= 236 mr = 1409 m= 17 mr = 134 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.800000 number of dielectric boundary points 70864 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 16016 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) : 2.113763 object centre at (A) : 48.90400 6.329000 25.18950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1281046 0.2259688 midg,1,midg; midg,igrid,midg 0.3713771 0.1417819 1,midg,midg; igrid,midg,midg 0.4212705 -0.5656381 gauss-seidel spectral radius is 0.9992965 estimated iterations to convergence 297 setup time was (sec) 2.110000 now iterating at: 06:03:04 rms-change max change #iterations 10.34519 331.7386 at 10iterations 6.125360 128.3603 at 20iterations 3.635941 83.87349 at 30iterations 2.144231 44.19471 at 40iterations 1.262470 22.57375 at 50iterations 0.7432020 14.79185 at 60iterations 0.4371377 7.922919 at 70iterations 0.2562366 4.298950 at 80iterations 0.1501597 2.490425 at 90iterations 8.8138439E-02 1.589951 at 100iterations 5.1800981E-02 0.8714886 at 110iterations 3.0516278E-02 0.5516548 at 120iterations 1.8059811E-02 0.3382797 at 130iterations 1.0781182E-02 0.1886482 at 140iterations 6.5561128E-03 0.1123619 at 150iterations 4.1029975E-03 7.5576782E-02 at 160iterations 2.7026972E-03 4.7466278E-02 at 170iterations 1.8856376E-03 3.7590027E-02 at 180iterations finished qdiffx linear iterations at : 06:03:15 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 1.8856376E-03 3.7590027E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 06:03:16 13.000u 0.291s 0:14.11 94.1% 0+0k 0+0io 0pf+0w