Tue Oct 11 07:51:05 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 07:51:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2376 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: 0.6435286 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): -9.067000 39.67500 ymin,ymax (A): -14.41300 40.90700 zmin,zma (A): 5.085000 52.57700 x,y,z range (A): 48.74200 55.32000 47.49200 scale (grids/A): 0.6435286 object centre (A): 15.30400 13.24700 28.83100 number of atom coordinates read : 2376 total number of charged atoms : 2240 net assigned charge : 4.500007 assigned positive charge : 356.3043 centred at (gu) : 89.49580 88.58570 90.65463 assigned negative charge : -351.8048 centred at (gu) : 89.41077 88.59817 90.81760 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6667 nv = 96 ne = 84 npr = 47978 no. pairs analyzed = 47978 no. exposed pairs = 2848 no. arc points = 19996 no. surface atoms = 967 nbur = 1409 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 385 mr = 3766 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2055 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7873 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2613476E-08 -1.3706819E-08 midg,1,midg; midg,igrid,midg 1.1920379E-08 4.4927426E-09 1,midg,midg; igrid,midg,midg -2.8778997E-09 1.5454225E-08 gauss-seidel spectral radius is 0.9874687 estimated iterations to convergence 73 setup time was (sec) 0.5400000 now iterating at: 07:51:05 rms-change max change #iterations 0.1422008 21.69836 at 10iterations 1.4679958E-02 1.930231 at 20iterations 1.5447182E-03 0.2530594 at 30iterations 1.8848846E-04 3.0099869E-02 at 40iterations 2.9192403E-05 4.8942566E-03 at 50iterations finished qdiffx linear iterations at : 07:51:09 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 2.9192403E-05 4.8942566E-03 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 07:51:10 4.424u 0.390s 0:05.19 92.6% 0+0k 0+0io 6pf+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 07:51:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2376 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: 1.930586 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): -9.067000 39.67500 ymin,ymax (A): -14.41300 40.90700 zmin,zma (A): 5.085000 52.57700 x,y,z range (A): 48.74200 55.32000 47.49200 scale (grids/A): 1.930586 object centre (A): 15.30400 13.24700 28.83100 number of atom coordinates read : 2376 total number of charged atoms : 2240 net assigned charge : 4.500007 assigned positive charge : 356.3043 centred at (gu) : 88.48714 85.75671 91.96376 assigned negative charge : -351.8048 centred at (gu) : 88.23218 85.79436 92.45261 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 71879 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19996 grid for indexing accessible points = 1.400000 m= 27457 mr = 50525 m= 4295 mr = 20737 m= 291 mr = 2839 m= 7 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1217 time to turn everything in is 0.6000000 number of dielectric boundary points 29715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17655 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) : 0.6435286 object centre at (A) : 15.30400 13.24700 28.83100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1190330E-02 -2.0743383E-02 midg,1,midg; midg,igrid,midg 3.0745097E-02 2.0324521E-02 1,midg,midg; igrid,midg,midg -3.3489300E-03 5.3304224E-03 gauss-seidel spectral radius is 0.9986479 estimated iterations to convergence 215 setup time was (sec) 0.9300000 now iterating at: 07:51:11 rms-change max change #iterations 4.053608 165.1731 at 10iterations 1.902811 73.58475 at 20iterations 0.9006283 29.29000 at 30iterations 0.4244960 12.54887 at 40iterations 0.1994984 6.575935 at 50iterations 9.3793005E-02 2.971316 at 60iterations 4.4314321E-02 1.452564 at 70iterations 2.0885168E-02 0.7001896 at 80iterations 9.8249903E-03 0.3110886 at 90iterations 4.6450752E-03 0.1396618 at 100iterations 2.1893091E-03 7.3669434E-02 at 110iterations 1.0356501E-03 3.4996510E-02 at 120iterations finished qdiffx linear iterations at : 07:51:21 total time elapsed so far: 10.61000 # loops : 120 mean,max change (kT/e) : 1.0356501E-03 3.4996510E-02 energy calculations done at 10.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.77000 DelPhi exited at 07:51:21 10.778u 0.473s 0:11.67 96.3% 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 07:51:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2376 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: 2.895879 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): -9.067000 39.67500 ymin,ymax (A): -14.41300 40.90700 zmin,zma (A): 5.085000 52.57700 x,y,z range (A): 48.74200 55.32000 47.49200 scale (grids/A): 2.895879 object centre (A): 15.30400 13.24700 28.83100 number of atom coordinates read : 2376 total number of charged atoms : 2240 net assigned charge : 4.500007 assigned positive charge : 356.3043 centred at (gu) : 87.73071 83.63494 92.94559 assigned negative charge : -351.8048 centred at (gu) : 87.34830 83.69155 93.67889 start vw surface at 0.1200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 165991 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19996 grid for indexing accessible points = 1.400000 m= 87717 mr = 121788 m= 32771 mr = 73048 m= 7821 mr = 26834 m= 1237 mr = 5941 m= 83 mr = 931 m= 0 mr = 38 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 4301 time to turn everything in is 1.550000 number of dielectric boundary points 67040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 17916 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) : 1.930586 object centre at (A) : 15.30400 13.24700 28.83100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4770114 -0.3448592 midg,1,midg; midg,igrid,midg 0.2553528 0.1954635 1,midg,midg; igrid,midg,midg -2.4261482E-02 -2.1238461E-02 gauss-seidel spectral radius is 0.9992541 estimated iterations to convergence 289 setup time was (sec) 1.880000 now iterating at: 07:51:24 rms-change max change #iterations 9.577088 369.7736 at 10iterations 5.577389 150.7041 at 20iterations 3.236603 80.08891 at 30iterations 1.871266 41.09871 at 40iterations 1.078416 21.11067 at 50iterations 0.6222179 12.33782 at 60iterations 0.3585176 7.935987 at 70iterations 0.2057935 4.183739 at 80iterations 0.1182641 2.364067 at 90iterations 6.8058193E-02 1.229118 at 100iterations 3.9024785E-02 0.6942406 at 110iterations 2.2481825E-02 0.4443665 at 120iterations 1.2886450E-02 0.2398400 at 130iterations 7.4121295E-03 0.1364479 at 140iterations 4.2708144E-03 7.5056076E-02 at 150iterations 2.4706314E-03 4.4862747E-02 at 160iterations 1.4366279E-03 2.6582718E-02 at 170iterations 8.4459438E-04 1.6139984E-02 at 180iterations finished qdiffx linear iterations at : 07:51:40 total time elapsed so far: 17.55000 # loops : 180 mean,max change (kT/e) : 8.4459438E-04 1.6139984E-02 energy calculations done at 17.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.71000 DelPhi exited at 07:51:40 17.714u 0.468s 0:18.88 96.2% 0+0k 0+0io 0pf+0w