Tue Oct 11 00:35:23 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 00:35:23 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2739 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5954671 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): 10.24500 64.06600 ymin,ymax (A): -3.385000 56.40000 zmin,zma (A): 9.782000 52.46200 x,y,z range (A): 53.82100 59.78500 42.68000 scale (grids/A): 0.5954671 object centre (A): 37.15550 26.50750 31.12200 number of atom coordinates read : 2739 total number of charged atoms : 2594 net assigned charge : 5.500015 assigned positive charge : 415.5206 centred at (gu) : 89.11749 91.87290 89.97290 assigned negative charge : -410.0212 centred at (gu) : 89.17084 91.63334 90.13129 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6327 nv = 96 ne = 84 npr = 55552 no. pairs analyzed = 55552 no. exposed pairs = 3297 no. arc points = 23016 no. surface atoms = 1107 nbur = 1632 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 285 mr = 3518 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2100000 number of dielectric boundary points 3077 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2271 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8010 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0789974E-09 -3.5077401E-09 midg,1,midg; midg,igrid,midg -4.1042507E-09 1.4877760E-08 1,midg,midg; igrid,midg,midg 4.4220094E-09 6.5671801E-11 gauss-seidel spectral radius is 0.9854131 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 00:35:23 rms-change max change #iterations 0.1097998 18.30858 at 10iterations 1.0192426E-02 1.538795 at 20iterations 1.5255735E-03 0.3843307 at 30iterations 4.2481328E-04 0.1100197 at 40iterations 1.3033599E-04 3.4179688E-02 at 50iterations finished qdiffx linear iterations at : 00:35:26 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.3033599E-04 3.4179688E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 00:35:27 3.348u 0.171s 0:03.98 88.1% 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 00:35:27 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2739 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.786401 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): 10.24500 64.06600 ymin,ymax (A): -3.385000 56.40000 zmin,zma (A): 9.782000 52.46200 x,y,z range (A): 53.82100 59.78500 42.68000 scale (grids/A): 1.786401 object centre (A): 37.15550 26.50750 31.12200 number of atom coordinates read : 2739 total number of charged atoms : 2594 net assigned charge : 5.500015 assigned positive charge : 415.5206 centred at (gu) : 87.35197 95.61798 89.91808 assigned negative charge : -410.0212 centred at (gu) : 87.51208 94.89956 90.39348 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23016 grid for indexing accessible points = 1.400000 m= 23526 mr = 48770 m= 3009 mr = 17326 m= 98 mr = 1757 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1288 time to turn everything in is 0.3400000 number of dielectric boundary points 28466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 20228 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) : 0.5954671 object centre at (A) : 37.15550 26.50750 31.12200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1305524E-02 4.5722192E-03 midg,1,midg; midg,igrid,midg -1.9942569E-02 1.8587027E-02 1,midg,midg; igrid,midg,midg -3.2551945E-03 3.7392480E-03 gauss-seidel spectral radius is 0.9984587 estimated iterations to convergence 202 setup time was (sec) 0.5600000 now iterating at: 00:35:27 rms-change max change #iterations 3.890903 162.3694 at 10iterations 1.725697 63.05182 at 20iterations 0.7709877 27.72963 at 30iterations 0.3446304 11.08612 at 40iterations 0.1545230 5.068390 at 50iterations 6.9262922E-02 2.501693 at 60iterations 3.1063860E-02 0.9443245 at 70iterations 1.4056716E-02 0.5052414 at 80iterations 6.4592110E-03 0.2384605 at 90iterations 3.0298478E-03 0.1147919 at 100iterations 1.5126977E-03 6.4868927E-02 at 110iterations 8.0779486E-04 3.5770416E-02 at 120iterations finished qdiffx linear iterations at : 00:35:34 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 8.0779486E-04 3.5770416E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 00:35:35 7.668u 0.181s 0:08.30 94.4% 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 Tue Oct 11 2011 at 00:35:35 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2739 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.679602 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): 10.24500 64.06600 ymin,ymax (A): -3.385000 56.40000 zmin,zma (A): 9.782000 52.46200 x,y,z range (A): 53.82100 59.78500 42.68000 scale (grids/A): 2.679602 object centre (A): 37.15550 26.50750 31.12200 number of atom coordinates read : 2739 total number of charged atoms : 2594 net assigned charge : 5.500015 assigned positive charge : 415.5206 centred at (gu) : 86.02774 98.42689 89.87687 assigned negative charge : -410.0212 centred at (gu) : 86.26817 97.34929 90.59013 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 161352 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23016 grid for indexing accessible points = 1.400000 m= 78985 mr = 118141 m= 25979 mr = 64801 m= 5203 mr = 20764 m= 465 mr = 3788 m= 13 mr = 233 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 4216 time to turn everything in is 0.8500000 number of dielectric boundary points 64265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 20749 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) : 1.786401 object centre at (A) : 37.15550 26.50750 31.12200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2319932 6.1917003E-02 midg,1,midg; midg,igrid,midg -0.3672473 -9.4051637E-02 1,midg,midg; igrid,midg,midg -9.4761774E-02 1.5901983E-02 gauss-seidel spectral radius is 0.9992059 estimated iterations to convergence 280 setup time was (sec) 1.080000 now iterating at: 00:35:36 rms-change max change #iterations 9.316953 265.4148 at 10iterations 5.298326 122.6862 at 20iterations 2.999919 70.49471 at 30iterations 1.692594 35.87412 at 40iterations 0.9551497 21.33525 at 50iterations 0.5375242 10.75144 at 60iterations 0.3033454 5.622081 at 70iterations 0.1708172 3.207486 at 80iterations 9.6145898E-02 1.839844 at 90iterations 5.4284289E-02 1.023594 at 100iterations 3.0572813E-02 0.5893955 at 110iterations 1.7317837E-02 0.3548126 at 120iterations 9.8961182E-03 0.2243271 at 130iterations 5.6884196E-03 0.1149979 at 140iterations 3.3274086E-03 8.3709717E-02 at 150iterations 2.0190172E-03 5.0563812E-02 at 160iterations 1.2846700E-03 3.2615662E-02 at 170iterations 8.6246995E-04 2.3399353E-02 at 180iterations finished qdiffx linear iterations at : 00:35:47 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 8.6246995E-04 2.3399353E-02 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 00:35:48 12.285u 0.211s 0:12.93 96.5% 0+0k 0+0io 0pf+0w