Tue Oct 11 04:51:09 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 04:51:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 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: 0.6294757 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): -72.58600 -16.41100 ymin,ymax (A): -48.76700 0.6270000 zmin,zma (A): 4.446000 61.00100 x,y,z range (A): 56.17500 49.39400 56.55500 scale (grids/A): 0.6294757 object centre (A): -44.49850 -24.07000 32.72350 number of atom coordinates read : 2859 total number of charged atoms : 2712 net assigned charge : 8.000020 assigned positive charge : 436.5795 centred at (gu) : 90.62046 90.42247 90.87696 assigned negative charge : -428.5803 centred at (gu) : 90.58308 90.15616 90.77870 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7515 nv = 96 ne = 84 npr = 56501 no. pairs analyzed = 56501 no. exposed pairs = 3751 no. arc points = 25316 no. surface atoms = 1259 nbur = 1600 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 4039 m= 2 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3300000 number of dielectric boundary points 3850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2503 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9078 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.1149510E-10 2.1424446E-08 midg,1,midg; midg,igrid,midg -1.6380721E-08 3.6460726E-08 1,midg,midg; igrid,midg,midg 4.1964214E-09 1.3637932E-08 gauss-seidel spectral radius is 0.9869509 estimated iterations to convergence 72 setup time was (sec) 0.5600000 now iterating at: 04:51:10 rms-change max change #iterations 0.1439648 20.77736 at 10iterations 1.3558494E-02 2.109804 at 20iterations 1.3336879E-03 0.2044983 at 30iterations 1.2969568E-04 1.7166138E-02 at 40iterations 1.3327204E-05 2.3574829E-03 at 50iterations finished qdiffx linear iterations at : 04:51:12 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.3327204E-05 2.3574829E-03 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 04:51:13 3.361u 0.147s 0:04.21 83.1% 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 04:51:13 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 = 2859 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.888427 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): -72.58600 -16.41100 ymin,ymax (A): -48.76700 0.6270000 zmin,zma (A): 4.446000 61.00100 x,y,z range (A): 56.17500 49.39400 56.55500 scale (grids/A): 1.888427 object centre (A): -44.49850 -24.07000 32.72350 number of atom coordinates read : 2859 total number of charged atoms : 2712 net assigned charge : 8.000020 assigned positive charge : 436.5795 centred at (gu) : 91.86070 91.26685 92.63034 assigned negative charge : -428.5803 centred at (gu) : 91.74896 90.46838 92.33574 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25316 grid for indexing accessible points = 1.400000 m= 29475 mr = 54849 m= 4801 mr = 21379 m= 258 mr = 2948 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1216 time to turn everything in is 0.6200000 number of dielectric boundary points 35577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 175 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 21250 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) : 0.6294757 object centre at (A) : -44.49850 -24.07000 32.72350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9224120E-02 4.3646522E-02 midg,1,midg; midg,igrid,midg -2.8323090E-02 5.9266642E-02 1,midg,midg; igrid,midg,midg -4.6498948E-03 -1.1774680E-02 gauss-seidel spectral radius is 0.9986464 estimated iterations to convergence 215 setup time was (sec) 0.9000000 now iterating at: 04:51:14 rms-change max change #iterations 4.438697 184.8073 at 10iterations 2.081590 86.55707 at 20iterations 0.9778863 35.09156 at 30iterations 0.4605934 13.21414 at 40iterations 0.2159795 6.474169 at 50iterations 0.1010701 3.336834 at 60iterations 4.7796719E-02 1.556733 at 70iterations 2.2472404E-02 0.6841607 at 80iterations 1.0538915E-02 0.3338280 at 90iterations 4.9514305E-03 0.1720581 at 100iterations 2.3426549E-03 7.3791504E-02 at 110iterations 1.1009185E-03 3.4788132E-02 at 120iterations finished qdiffx linear iterations at : 04:51:21 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 1.1009185E-03 3.4788132E-02 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 04:51:22 7.502u 0.163s 0:08.33 91.9% 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 04:51:22 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 = 2859 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: 2.832641 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): -72.58600 -16.41100 ymin,ymax (A): -48.76700 0.6270000 zmin,zma (A): 4.446000 61.00100 x,y,z range (A): 56.17500 49.39400 56.55500 scale (grids/A): 2.832641 object centre (A): -44.49850 -24.07000 32.72350 number of atom coordinates read : 2859 total number of charged atoms : 2712 net assigned charge : 8.000020 assigned positive charge : 436.5795 centred at (gu) : 92.79095 91.90009 93.94534 assigned negative charge : -428.5803 centred at (gu) : 92.62331 90.70235 93.50364 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 185481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25316 grid for indexing accessible points = 1.400000 m= 94326 mr = 133158 m= 34744 mr = 76036 m= 8468 mr = 27656 m= 1128 mr = 6315 m= 61 mr = 704 m= 0 mr = 19 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 4286 time to turn everything in is 1.540000 number of dielectric boundary points 80320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 21691 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) : 1.888427 object centre at (A) : -44.49850 -24.07000 32.72350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1276892 0.3407412 midg,1,midg; midg,igrid,midg -0.3195699 0.5117137 1,midg,midg; igrid,midg,midg -0.2011145 -0.1344852 gauss-seidel spectral radius is 0.9992679 estimated iterations to convergence 292 setup time was (sec) 1.850000 now iterating at: 04:51:24 rms-change max change #iterations 10.39063 350.7961 at 10iterations 6.100028 125.1988 at 20iterations 3.554616 81.54906 at 30iterations 2.071745 42.36846 at 40iterations 1.200600 23.15213 at 50iterations 0.6980488 13.38446 at 60iterations 0.4046614 7.206050 at 70iterations 0.2339010 4.076828 at 80iterations 0.1352179 2.407547 at 90iterations 7.8190282E-02 1.477647 at 100iterations 4.5177221E-02 0.7945423 at 110iterations 2.6120132E-02 0.4502640 at 120iterations 1.5064511E-02 0.2596092 at 130iterations 8.6828573E-03 0.1581841 at 140iterations 5.0334139E-03 9.0991974E-02 at 150iterations 2.9098811E-03 5.8692932E-02 at 160iterations 1.6816666E-03 3.0502319E-02 at 170iterations 9.7246148E-04 1.7700195E-02 at 180iterations finished qdiffx linear iterations at : 04:51:34 total time elapsed so far: 12.09000 # loops : 180 mean,max change (kT/e) : 9.7246148E-04 1.7700195E-02 energy calculations done at 12.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 04:51:35 12.277u 0.177s 0:12.99 95.7% 0+0k 0+0io 0pf+0w