Tue Oct 11 08:04:07 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 08:04:07 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2632 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.6027973 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): 2.563000 58.98700 ymin,ymax (A): 7.118000 65.77500 zmin,zma (A): -22.80300 36.25500 x,y,z range (A): 56.42400 58.65700 59.05800 scale (grids/A): 0.6027973 object centre (A): 30.77500 36.44650 6.726001 number of atom coordinates read : 2632 total number of charged atoms : 2489 net assigned charge : 7.000020 assigned positive charge : 391.4096 centred at (gu) : 89.95188 90.00882 91.01221 assigned negative charge : -384.4104 centred at (gu) : 89.76553 90.09905 90.96722 start vw surface at 0.2100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6319 nv = 96 ne = 84 npr = 52801 no. pairs analyzed = 52801 no. exposed pairs = 3404 no. arc points = 23796 no. surface atoms = 1157 nbur = 1475 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 298 mr = 3222 m= 0 mr = 26 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2432 ## 281 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7904 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2158656E-09 6.3204935E-09 midg,1,midg; midg,igrid,midg 6.7787371E-09 -3.1669090E-10 1,midg,midg; igrid,midg,midg -4.2731210E-09 1.0345925E-08 gauss-seidel spectral radius is 0.9857626 estimated iterations to convergence 69 setup time was (sec) 0.5900000 now iterating at: 08:04:08 rms-change max change #iterations 0.1091771 14.98833 at 10iterations 9.3275439E-03 1.349293 at 20iterations 8.0581184E-04 0.1193695 at 30iterations 6.9649504E-05 1.1703491E-02 at 40iterations 5.8611513E-06 9.0026855E-04 at 50iterations finished qdiffx linear iterations at : 08:04:10 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 5.8611513E-06 9.0026855E-04 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 08:04:11 3.363u 0.193s 0:03.90 91.0% 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 08:04:11 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2632 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.808392 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): 2.563000 58.98700 ymin,ymax (A): 7.118000 65.77500 zmin,zma (A): -22.80300 36.25500 x,y,z range (A): 56.42400 58.65700 59.05800 scale (grids/A): 1.808392 object centre (A): 30.77500 36.44650 6.726001 number of atom coordinates read : 2632 total number of charged atoms : 2489 net assigned charge : 7.000020 assigned positive charge : 391.4096 centred at (gu) : 89.85525 90.02579 93.03612 assigned negative charge : -384.4104 centred at (gu) : 89.29633 90.29691 92.90150 start vw surface at 0.2300000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 69076 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23796 grid for indexing accessible points = 1.400000 m= 22126 mr = 46236 m= 2794 mr = 15420 m= 114 mr = 1548 m= 0 mr = 36 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 635 time to turn everything in is 0.5800000 number of dielectric boundary points 30870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19424 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) : 0.6027973 object centre at (A) : 30.77500 36.44650 6.726001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6498667E-03 3.9034549E-02 midg,1,midg; midg,igrid,midg 1.4077661E-02 -1.1979797E-02 1,midg,midg; igrid,midg,midg -2.7416386E-02 1.5580812E-02 gauss-seidel spectral radius is 0.9984912 estimated iterations to convergence 204 setup time was (sec) 0.8900000 now iterating at: 08:04:12 rms-change max change #iterations 3.796688 171.9816 at 10iterations 1.703804 68.85437 at 20iterations 0.7645918 27.03679 at 30iterations 0.3436686 12.05859 at 40iterations 0.1542371 5.332125 at 50iterations 6.9347858E-02 2.178419 at 60iterations 3.1167928E-02 1.132248 at 70iterations 1.4045414E-02 0.4602675 at 80iterations 6.3163969E-03 0.2107353 at 90iterations 2.8437474E-03 0.1053336 at 100iterations 1.2753897E-03 4.8080146E-02 at 110iterations 5.7623890E-04 2.1533489E-02 at 120iterations finished qdiffx linear iterations at : 08:04:18 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 5.7623890E-04 2.1533489E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 08:04:19 7.627u 0.220s 0:08.37 93.6% 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 08:04:19 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2632 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: 2.712588 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): 2.563000 58.98700 ymin,ymax (A): 7.118000 65.77500 zmin,zma (A): -22.80300 36.25500 x,y,z range (A): 56.42400 58.65700 59.05800 scale (grids/A): 2.712588 object centre (A): 30.77500 36.44650 6.726001 number of atom coordinates read : 2632 total number of charged atoms : 2489 net assigned charge : 7.000020 assigned positive charge : 391.4096 centred at (gu) : 89.78266 90.03848 94.55411 assigned negative charge : -384.4104 centred at (gu) : 88.94444 90.44537 94.35207 start vw surface at 0.1900000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 159987 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23796 grid for indexing accessible points = 1.400000 m= 74552 mr = 112949 m= 23355 mr = 59050 m= 4769 mr = 17936 m= 555 mr = 3355 m= 27 mr = 342 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 2082 time to turn everything in is 1.250000 number of dielectric boundary points 69608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 19901 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) : 1.808392 object centre at (A) : 30.77500 36.44650 6.726001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5538038E-02 0.3890239 midg,1,midg; midg,igrid,midg 9.3087889E-02 -6.2023681E-02 1,midg,midg; igrid,midg,midg -0.3810160 0.2694017 gauss-seidel spectral radius is 0.9992239 estimated iterations to convergence 283 setup time was (sec) 1.550000 now iterating at: 08:04:21 rms-change max change #iterations 9.218676 292.3281 at 10iterations 5.335327 118.5868 at 20iterations 3.065351 74.39405 at 30iterations 1.748078 35.64068 at 40iterations 0.9979341 20.23505 at 50iterations 0.5674343 12.70900 at 60iterations 0.3226612 6.851707 at 70iterations 0.1834019 3.450058 at 80iterations 0.1040475 2.385165 at 90iterations 5.8844291E-02 1.179545 at 100iterations 3.3323601E-02 0.6383934 at 110iterations 1.8960511E-02 0.3753529 at 120iterations 1.0706102E-02 0.2227826 at 130iterations 6.0659754E-03 0.1265445 at 140iterations 3.4269507E-03 6.8384171E-02 at 150iterations 1.9423849E-03 3.9012909E-02 at 160iterations 1.0998965E-03 2.1080971E-02 at 170iterations 6.2344573E-04 1.1949062E-02 at 180iterations finished qdiffx linear iterations at : 08:04:31 total time elapsed so far: 11.72000 # loops : 180 mean,max change (kT/e) : 6.2344573E-04 1.1949062E-02 energy calculations done at 11.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.89000 DelPhi exited at 08:04:32 11.895u 0.224s 0:12.48 97.0% 0+0k 0+0io 0pf+0w