Tue Oct 11 03:45:11 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 03:45:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 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: 0.6607153 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): 36.97400 85.66199 ymin,ymax (A): -4.833000 49.04800 zmin,zma (A): -15.73500 33.91400 x,y,z range (A): 48.68799 53.88100 49.64900 scale (grids/A): 0.6607153 object centre (A): 61.31800 22.10750 9.089499 number of atom coordinates read : 2762 total number of charged atoms : 2615 net assigned charge : 5.500017 assigned positive charge : 418.6837 centred at (gu) : 88.65723 90.60508 90.52230 assigned negative charge : -413.1843 centred at (gu) : 88.83123 90.35944 90.53831 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8054 nv = 96 ne = 84 npr = 56532 no. pairs analyzed = 56532 no. exposed pairs = 3279 no. arc points = 22693 no. surface atoms = 1102 nbur = 1660 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 495 mr = 4645 m= 3 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 0.3700000 number of dielectric boundary points 3836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2250 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9554 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5169956E-08 1.1072899E-08 midg,1,midg; midg,igrid,midg -3.5617862E-08 7.3482468E-08 1,midg,midg; igrid,midg,midg 6.6365601E-08 -1.8322975E-08 gauss-seidel spectral radius is 0.9881378 estimated iterations to convergence 75 setup time was (sec) 0.6500000 now iterating at: 03:45:12 rms-change max change #iterations 0.1774234 26.06121 at 10iterations 1.8913476E-02 2.763226 at 20iterations 2.1131474E-03 0.2749424 at 30iterations 2.4492503E-04 2.8839111E-02 at 40iterations 4.1869022E-05 7.2364807E-03 at 50iterations finished qdiffx linear iterations at : 03:45:16 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 4.1869022E-05 7.2364807E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 03:45:16 4.128u 0.289s 0:04.81 91.4% 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 03:45:16 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 = 2762 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: 1.982146 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): 36.97400 85.66199 ymin,ymax (A): -4.833000 49.04800 zmin,zma (A): -15.73500 33.91400 x,y,z range (A): 48.68799 53.88100 49.64900 scale (grids/A): 1.982146 object centre (A): 61.31800 22.10750 9.089499 number of atom coordinates read : 2762 total number of charged atoms : 2615 net assigned charge : 5.500017 assigned positive charge : 418.6837 centred at (gu) : 85.97133 91.81461 91.56653 assigned negative charge : -413.1843 centred at (gu) : 86.49349 91.07793 91.61486 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 85920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22693 grid for indexing accessible points = 1.400000 m= 33515 mr = 60977 m= 5912 mr = 25539 m= 351 mr = 3921 m= 3 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 677 time to turn everything in is 0.7700000 number of dielectric boundary points 35106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 20654 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) : 0.6607153 object centre at (A) : 61.31800 22.10750 9.089499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4928161E-03 -5.3896327E-03 midg,1,midg; midg,igrid,midg -6.0210399E-02 5.9790406E-02 1,midg,midg; igrid,midg,midg 0.1126913 -2.6491026E-03 gauss-seidel spectral radius is 0.9987476 estimated iterations to convergence 224 setup time was (sec) 1.070000 now iterating at: 03:45:18 rms-change max change #iterations 4.777699 188.1617 at 10iterations 2.322234 73.60150 at 20iterations 1.124315 33.79633 at 30iterations 0.5463613 15.98430 at 40iterations 0.2651386 7.905937 at 50iterations 0.1285848 3.866907 at 60iterations 6.2221531E-02 1.796458 at 70iterations 3.0279616E-02 0.9153099 at 80iterations 1.4634096E-02 0.3977127 at 90iterations 7.1208458E-03 0.2216072 at 100iterations 3.4422146E-03 9.7038269E-02 at 110iterations 1.6759037E-03 5.5239201E-02 at 120iterations finished qdiffx linear iterations at : 03:45:26 total time elapsed so far: 9.630000 # loops : 120 mean,max change (kT/e) : 1.6759037E-03 5.5239201E-02 energy calculations done at 9.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.800000 DelPhi exited at 03:45:27 9.807u 0.328s 0:10.54 96.0% 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 03:45:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 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: 2.973219 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): 36.97400 85.66199 ymin,ymax (A): -4.833000 49.04800 zmin,zma (A): -15.73500 33.91400 x,y,z range (A): 48.68799 53.88100 49.64900 scale (grids/A): 2.973219 object centre (A): 61.31800 22.10750 9.089499 number of atom coordinates read : 2762 total number of charged atoms : 2615 net assigned charge : 5.500017 assigned positive charge : 418.6837 centred at (gu) : 83.95660 92.72189 92.34969 assigned negative charge : -413.1843 centred at (gu) : 84.74020 91.61697 92.42220 start vw surface at 0.1500000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 198069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22693 grid for indexing accessible points = 1.400000 m= 106014 mr = 146807 m= 41694 mr = 88315 m= 10842 mr = 34361 m= 1695 mr = 8457 m= 86 mr = 1183 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 2232 time to turn everything in is 2.010000 number of dielectric boundary points 79232 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 20920 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) : 1.982146 object centre at (A) : 61.31800 22.10750 9.089499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5110979E-02 -6.2000230E-02 midg,1,midg; midg,igrid,midg -0.5791769 0.1630666 1,midg,midg; igrid,midg,midg 1.152729 -5.0780784E-02 gauss-seidel spectral radius is 0.9992883 estimated iterations to convergence 296 setup time was (sec) 2.340000 now iterating at: 03:45:30 rms-change max change #iterations 10.86818 373.5983 at 10iterations 6.424743 174.0456 at 20iterations 3.786763 77.30789 at 30iterations 2.230850 44.19144 at 40iterations 1.308272 24.71189 at 50iterations 0.7658540 13.77084 at 60iterations 0.4486910 8.005822 at 70iterations 0.2621780 4.704888 at 80iterations 0.1531034 3.021557 at 90iterations 8.9355625E-02 1.429703 at 100iterations 5.2115504E-02 0.9127638 at 110iterations 3.0411750E-02 0.5309572 at 120iterations 1.7667204E-02 0.2898655 at 130iterations 1.0337355E-02 0.1929855 at 140iterations 6.0479348E-03 9.9114597E-02 at 150iterations 3.5360048E-03 5.5507660E-02 at 160iterations 2.0795970E-03 3.7399292E-02 at 170iterations 1.2318079E-03 2.1453857E-02 at 180iterations finished qdiffx linear iterations at : 03:45:44 total time elapsed so far: 16.82000 # loops : 180 mean,max change (kT/e) : 1.2318079E-03 2.1453857E-02 energy calculations done at 16.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.00000 DelPhi exited at 03:45:45 17.000u 0.346s 0:18.10 95.8% 0+0k 0+0io 0pf+0w