Tue Oct 11 06:08:44 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 06:08:44 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 = 2016 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: 0.7479150 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): -8.862000 35.22500 ymin,ymax (A): -3.661000 34.03100 zmin,zma (A): 2.011000 49.61000 x,y,z range (A): 44.08700 37.69200 47.59900 scale (grids/A): 0.7479150 object centre (A): 13.18150 15.18500 25.81050 number of atom coordinates read : 2016 total number of charged atoms : 1888 net assigned charge : 6.500006 assigned positive charge : 304.5301 centred at (gu) : 90.11739 89.54230 91.15121 assigned negative charge : -298.0302 centred at (gu) : 89.93292 89.60381 91.22019 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7843 nv = 96 ne = 84 npr = 40381 no. pairs analyzed = 40381 no. exposed pairs = 2410 no. arc points = 16644 no. surface atoms = 823 nbur = 1193 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 611 mr = 4566 m= 7 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3753 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1506 ## 138 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8216 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7222941E-07 7.1538359E-08 midg,1,midg; midg,igrid,midg 2.2182455E-07 6.2703393E-08 1,midg,midg; igrid,midg,midg -7.0106687E-08 3.4459129E-07 gauss-seidel spectral radius is 0.9906685 estimated iterations to convergence 84 setup time was (sec) 0.5500000 now iterating at: 06:08:45 rms-change max change #iterations 0.2450020 31.88811 at 10iterations 3.3607405E-02 4.188742 at 20iterations 4.7685788E-03 0.5942173 at 30iterations 7.2325423E-04 9.7583771E-02 at 40iterations 1.4304310E-04 1.8158436E-02 at 50iterations finished qdiffx linear iterations at : 06:08:49 total time elapsed so far: 4.240000 # loops : 50 mean,max change (kT/e) : 1.4304310E-04 1.8158436E-02 energy calculations done at 4.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 06:08:49 4.419u 0.394s 0:05.41 88.7% 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 06:08:50 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 = 2016 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: 2.243745 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): -8.862000 35.22500 ymin,ymax (A): -3.661000 34.03100 zmin,zma (A): 2.011000 49.61000 x,y,z range (A): 44.08700 37.69200 47.59900 scale (grids/A): 2.243745 object centre (A): 13.18150 15.18500 25.81050 number of atom coordinates read : 2016 total number of charged atoms : 1888 net assigned charge : 6.500006 assigned positive charge : 304.5301 centred at (gu) : 90.35220 88.62697 93.45378 assigned negative charge : -298.0302 centred at (gu) : 89.79896 88.81138 93.66077 start vw surface at 0.1000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 82137 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16644 grid for indexing accessible points = 1.400000 m= 35570 mr = 58781 m= 8270 mr = 27649 m= 932 mr = 5834 m= 27 mr = 539 m= 0 mr = 7 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 34126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 15034 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) : 0.7479150 object centre at (A) : 13.18150 15.18500 25.81050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7207033E-02 7.2162021E-03 midg,1,midg; midg,igrid,midg 4.4223800E-02 1.0871561E-02 1,midg,midg; igrid,midg,midg 3.7016191E-02 6.5359324E-02 gauss-seidel spectral radius is 0.9989316 estimated iterations to convergence 242 setup time was (sec) 1.040000 now iterating at: 06:08:51 rms-change max change #iterations 4.935842 212.9371 at 10iterations 2.532416 80.98926 at 20iterations 1.296469 36.34459 at 30iterations 0.6646013 19.23317 at 40iterations 0.3421599 9.313852 at 50iterations 0.1752202 4.852703 at 60iterations 8.9861579E-02 2.501186 at 70iterations 4.5841005E-02 1.271069 at 80iterations 2.3544680E-02 0.6298137 at 90iterations 1.2145527E-02 0.3640528 at 100iterations 6.2471796E-03 0.1960373 at 110iterations 3.2289766E-03 9.2299461E-02 at 120iterations finished qdiffx linear iterations at : 06:09:00 total time elapsed so far: 10.54000 # loops : 120 mean,max change (kT/e) : 3.2289766E-03 9.2299461E-02 energy calculations done at 10.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.71000 DelPhi exited at 06:09:01 10.711u 0.442s 0:11.68 95.4% 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 06:09:01 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 = 2016 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: 3.365617 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): -8.862000 35.22500 ymin,ymax (A): -3.661000 34.03100 zmin,zma (A): 2.011000 49.61000 x,y,z range (A): 44.08700 37.69200 47.59900 scale (grids/A): 3.365617 object centre (A): 13.18150 15.18500 25.81050 number of atom coordinates read : 2016 total number of charged atoms : 1888 net assigned charge : 6.500006 assigned positive charge : 304.5301 centred at (gu) : 90.52840 87.94044 95.18079 assigned negative charge : -298.0302 centred at (gu) : 89.69829 88.21713 95.49123 start vw surface at 0.1000000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 188967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16644 grid for indexing accessible points = 1.400000 m= 106988 mr = 140808 m= 48408 mr = 90251 m= 16174 mr = 40685 m= 3766 mr = 13064 m= 586 mr = 2840 m= 21 mr = 426 m= 0 mr = 10 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.200000 number of dielectric boundary points 76826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.330000 number of grid points assigned charge 15104 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) : 2.243745 object centre at (A) : 13.18150 15.18500 25.81050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4247169 -2.7759835E-02 midg,1,midg; midg,igrid,midg 0.3326952 7.1458295E-02 1,midg,midg; igrid,midg,midg 0.5164369 0.4462656 gauss-seidel spectral radius is 0.9993204 estimated iterations to convergence 303 setup time was (sec) 2.520000 now iterating at: 06:09:04 rms-change max change #iterations 10.70301 309.0647 at 10iterations 6.411499 129.3146 at 20iterations 3.830115 69.33736 at 30iterations 2.283716 39.19689 at 40iterations 1.357778 24.67242 at 50iterations 0.8053549 15.02941 at 60iterations 0.4778555 9.212555 at 70iterations 0.2827368 5.015950 at 80iterations 0.1675510 2.803192 at 90iterations 9.9028274E-02 1.637504 at 100iterations 5.8692425E-02 0.9307880 at 110iterations 3.4673892E-02 0.5421724 at 120iterations 2.0659322E-02 0.3690672 at 130iterations 1.2353969E-02 0.2084818 at 140iterations 7.4858502E-03 0.1262894 at 150iterations 4.6484824E-03 7.9590797E-02 at 160iterations 2.9725034E-03 5.2150726E-02 at 170iterations 2.0076607E-03 3.5484314E-02 at 180iterations finished qdiffx linear iterations at : 06:09:20 total time elapsed so far: 18.46000 # loops : 180 mean,max change (kT/e) : 2.0076607E-03 3.5484314E-02 energy calculations done at 18.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.62000 DelPhi exited at 06:09:21 18.623u 0.484s 0:19.41 98.4% 0+0k 0+0io 0pf+0w