Sun Oct 9 00:38:54 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 00:38:54 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2442 !!! WARNING: GLM 131 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6184636 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): -13.19200 40.72400 ymin,ymax (A): -32.33900 25.22300 zmin,zma (A): -9.628000 33.59400 x,y,z range (A): 53.91600 57.56200 43.22200 scale (grids/A): 0.6184636 object centre (A): 13.76600 -3.558001 11.98300 number of atom coordinates read : 2442 total number of charged atoms : 2303 net assigned charge : 11.40602 assigned positive charge : 356.1592 centred at (gu) : 89.79117 91.37526 90.42185 assigned negative charge : -344.7539 centred at (gu) : 89.78788 91.37772 90.37927 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6325 nv = 96 ne = 84 npr = 48700 no. pairs analyzed = 48700 no. exposed pairs = 3199 no. arc points = 22909 no. surface atoms = 1070 nbur = 1372 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3280 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.3500000 number of dielectric boundary points 3336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2286 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7704 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7913243E-09 1.2185984E-08 midg,1,midg; midg,igrid,midg 6.6317378E-09 1.1550079E-08 1,midg,midg; igrid,midg,midg 8.9385290E-09 8.5313605E-09 gauss-seidel spectral radius is 0.9864560 estimated iterations to convergence 70 setup time was (sec) 0.6300000 now iterating at: 00:38:55 rms-change max change #iterations 0.1198790 18.29787 at 10iterations 1.1143934E-02 1.842133 at 20iterations 1.1350880E-03 0.1903610 at 30iterations 2.0851815E-04 4.1831970E-02 at 40iterations 6.3185340E-05 1.4004707E-02 at 50iterations finished qdiffx linear iterations at : 00:38:58 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 6.3185340E-05 1.4004707E-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 00:38:58 4.167u 0.237s 0:04.70 93.4% 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 00:38:58 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2442 !!! WARNING: GLM 131 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.855391 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): -13.19200 40.72400 ymin,ymax (A): -32.33900 25.22300 zmin,zma (A): -9.628000 33.59400 x,y,z range (A): 53.91600 57.56200 43.22200 scale (grids/A): 1.855391 object centre (A): 13.76600 -3.558001 11.98300 number of atom coordinates read : 2442 total number of charged atoms : 2303 net assigned charge : 11.40602 assigned positive charge : 356.1592 centred at (gu) : 89.37294 94.12553 91.26514 assigned negative charge : -344.7539 centred at (gu) : 89.36364 94.13305 91.13802 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68581 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22909 grid for indexing accessible points = 1.400000 m= 22879 mr = 46010 m= 3313 mr = 16137 m= 152 mr = 1846 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1117 time to turn everything in is 0.5800000 number of dielectric boundary points 30896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 18026 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) : 0.6184636 object centre at (A) : 13.76600 -3.558001 11.98300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3265251E-03 1.7070225E-02 midg,1,midg; midg,igrid,midg 3.2644499E-02 3.2450046E-02 1,midg,midg; igrid,midg,midg 3.5105631E-02 3.5700053E-02 gauss-seidel spectral radius is 0.9985580 estimated iterations to convergence 209 setup time was (sec) 0.9200000 now iterating at: 00:39:00 rms-change max change #iterations 3.824131 229.6988 at 10iterations 1.741349 62.55566 at 20iterations 0.7958180 31.16848 at 30iterations 0.3648869 12.70622 at 40iterations 0.1667339 5.993695 at 50iterations 7.6412633E-02 2.508497 at 60iterations 3.5067137E-02 1.169220 at 70iterations 1.6152577E-02 0.5337358 at 80iterations 7.4399053E-03 0.2513123 at 90iterations 3.4568293E-03 0.1173916 at 100iterations 1.6428092E-03 5.7102203E-02 at 110iterations 8.1561832E-04 3.7426949E-02 at 120iterations finished qdiffx linear iterations at : 00:39:08 total time elapsed so far: 9.250000 # loops : 120 mean,max change (kT/e) : 8.1561832E-04 3.7426949E-02 energy calculations done at 9.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.430000 DelPhi exited at 00:39:08 9.431u 0.264s 0:10.01 96.8% 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 00:39:09 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2442 !!! WARNING: GLM 131 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.783086 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): -13.19200 40.72400 ymin,ymax (A): -32.33900 25.22300 zmin,zma (A): -9.628000 33.59400 x,y,z range (A): 53.91600 57.56200 43.22200 scale (grids/A): 2.783086 object centre (A): 13.76600 -3.558001 11.98300 number of atom coordinates read : 2442 total number of charged atoms : 2303 net assigned charge : 11.40602 assigned positive charge : 356.1592 centred at (gu) : 89.05937 96.18813 91.89749 assigned negative charge : -344.7539 centred at (gu) : 89.04541 96.19955 91.70693 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 158686 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22909 grid for indexing accessible points = 1.400000 m= 75847 mr = 112088 m= 25287 mr = 60376 m= 5611 mr = 19600 m= 748 mr = 3942 m= 26 mr = 488 m= 0 mr = 10 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 3508 time to turn everything in is 1.400000 number of dielectric boundary points 69701 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 18418 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) : 1.855391 object centre at (A) : 13.76600 -3.558001 11.98300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0069696E-02 0.1695977 midg,1,midg; midg,igrid,midg 0.4646948 0.3906595 1,midg,midg; igrid,midg,midg 0.3488972 0.4481180 gauss-seidel spectral radius is 0.9992416 estimated iterations to convergence 287 setup time was (sec) 1.730000 now iterating at: 00:39:10 rms-change max change #iterations 9.207233 314.0932 at 10iterations 5.377095 133.8266 at 20iterations 3.117896 66.99044 at 30iterations 1.807160 40.48393 at 40iterations 1.041486 21.60164 at 50iterations 0.5988299 12.98737 at 60iterations 0.3437236 6.823529 at 70iterations 0.1973793 3.932529 at 80iterations 0.1131972 2.208313 at 90iterations 6.4895824E-02 1.256724 at 100iterations 3.7089951E-02 0.8077669 at 110iterations 2.1195527E-02 0.4603729 at 120iterations 1.2162778E-02 0.2479820 at 130iterations 6.9723139E-03 0.1436958 at 140iterations 4.0285676E-03 8.7905884E-02 at 150iterations 2.3265684E-03 4.8328400E-02 at 160iterations 1.3672442E-03 3.1053543E-02 at 170iterations 8.2923949E-04 2.0050049E-02 at 180iterations finished qdiffx linear iterations at : 00:39:24 total time elapsed so far: 15.01000 # loops : 180 mean,max change (kT/e) : 8.2923949E-04 2.0050049E-02 energy calculations done at 15.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.19000 DelPhi exited at 00:39:24 15.187u 0.264s 0:15.72 98.2% 0+0k 0+0io 0pf+0w