Tue Oct 11 03:24:00 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 03:24:00 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1174 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7451596 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): -6.781000 29.14500 ymin,ymax (A): 1.174000 41.15700 zmin,zma (A): -1.587000 46.18800 x,y,z range (A): 35.92600 39.98300 47.77500 scale (grids/A): 0.7451596 object centre (A): 11.18200 21.16550 22.30050 number of atom coordinates read : 1174 total number of charged atoms : 1052 net assigned charge : 5.500003 assigned positive charge : 173.7531 centred at (gu) : 89.93595 88.63258 88.41270 assigned negative charge : -168.2531 centred at (gu) : 89.63053 88.61054 88.43600 start vw surface at 5.9999999E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 4561 nv = 96 ne = 84 npr = 22810 no. pairs analyzed = 22810 no. exposed pairs = 1525 no. arc points = 11273 no. surface atoms = 512 nbur = 662 mkacc time = 4.0000003E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 284 mr = 2374 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 5.0000001E-02 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.1100000 number of dielectric boundary points 2427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 917 ## 76 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 4521 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6289059E-07 7.1515188E-08 midg,1,midg; midg,igrid,midg 1.2162580E-07 9.4971803E-08 1,midg,midg; igrid,midg,midg -7.8430311E-08 2.8009552E-07 gauss-seidel spectral radius is 0.9905196 estimated iterations to convergence 83 setup time was (sec) 0.3000000 now iterating at: 03:24:01 rms-change max change #iterations 0.1776484 29.59732 at 10iterations 2.4040204E-02 4.317551 at 20iterations 3.2155795E-03 0.5517941 at 30iterations 4.2717368E-04 6.8199158E-02 at 40iterations 5.7324625E-05 1.0227203E-02 at 50iterations finished qdiffx linear iterations at : 03:24:04 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 5.7324625E-05 1.0227203E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 03:24:04 3.283u 0.165s 0:03.74 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 03:24:04 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1174 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.235479 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): -6.781000 29.14500 ymin,ymax (A): 1.174000 41.15700 zmin,zma (A): -1.587000 46.18800 x,y,z range (A): 35.92600 39.98300 47.77500 scale (grids/A): 2.235479 object centre (A): 11.18200 21.16550 22.30050 number of atom coordinates read : 1174 total number of charged atoms : 1052 net assigned charge : 5.500003 assigned positive charge : 173.7531 centred at (gu) : 89.80795 85.89785 85.23823 assigned negative charge : -168.2531 centred at (gu) : 88.89179 85.83183 85.30810 start vw surface at 5.0000001E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 47024 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11273 grid for indexing accessible points = 1.400000 m= 17895 mr = 30641 m= 3536 mr = 13430 m= 366 mr = 2342 m= 10 mr = 192 m= 0 mr = 4 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 900 time to turn everything in is 0.2400000 number of dielectric boundary points 22222 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8396 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) : 0.7451596 object centre at (A) : 11.18200 21.16550 22.30050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4829507E-02 1.3452063E-02 midg,1,midg; midg,igrid,midg 4.2089403E-02 3.0495021E-02 1,midg,midg; igrid,midg,midg -2.2567071E-02 4.5460291E-02 gauss-seidel spectral radius is 0.9988497 estimated iterations to convergence 233 setup time was (sec) 0.4600000 now iterating at: 03:24:05 rms-change max change #iterations 3.643708 249.3006 at 10iterations 1.810302 85.53304 at 20iterations 0.9015288 35.28535 at 30iterations 0.4477197 17.73659 at 40iterations 0.2228478 9.563145 at 50iterations 0.1109387 4.143321 at 60iterations 5.5015486E-02 1.948505 at 70iterations 2.7348084E-02 1.017578 at 80iterations 1.3640156E-02 0.5707761 at 90iterations 6.7481683E-03 0.2348938 at 100iterations 3.3515382E-03 0.1194801 at 110iterations 1.6706589E-03 6.8025589E-02 at 120iterations finished qdiffx linear iterations at : 03:24:12 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 1.6706589E-03 6.8025589E-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) 7.520000 DelPhi exited at 03:24:12 7.526u 0.196s 0:08.10 95.1% 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 03:24:12 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1174 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.353218 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): -6.781000 29.14500 ymin,ymax (A): 1.174000 41.15700 zmin,zma (A): -1.587000 46.18800 x,y,z range (A): 35.92600 39.98300 47.77500 scale (grids/A): 3.353218 object centre (A): 11.18200 21.16550 22.30050 number of atom coordinates read : 1174 total number of charged atoms : 1052 net assigned charge : 5.500003 assigned positive charge : 173.7531 centred at (gu) : 89.71192 83.84679 82.85734 assigned negative charge : -168.2531 centred at (gu) : 88.33766 83.74780 82.96216 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 107941 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11273 grid for indexing accessible points = 1.400000 m= 54980 mr = 74007 m= 23049 mr = 44940 m= 6654 mr = 18904 m= 1418 mr = 5100 m= 207 mr = 1052 m= 20 mr = 149 m= 0 mr = 20 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2638 time to turn everything in is 0.7400000 number of dielectric boundary points 50097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 8416 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) : 2.235479 object centre at (A) : 11.18200 21.16550 22.30050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2100644 9.1491409E-02 midg,1,midg; midg,igrid,midg 0.3750357 0.2690994 1,midg,midg; igrid,midg,midg -0.1753060 0.3216278 gauss-seidel spectral radius is 0.9992966 estimated iterations to convergence 297 setup time was (sec) 0.9700000 now iterating at: 03:24:14 rms-change max change #iterations 7.903017 273.0531 at 10iterations 4.611040 125.7444 at 20iterations 2.672603 64.50757 at 30iterations 1.549751 35.20157 at 40iterations 0.8994785 20.94884 at 50iterations 0.5227056 10.44839 at 60iterations 0.3025969 6.170624 at 70iterations 0.1758592 3.551910 at 80iterations 0.1021624 2.348379 at 90iterations 5.9065111E-02 1.292745 at 100iterations 3.4290772E-02 0.7188263 at 110iterations 1.9955551E-02 0.4219999 at 120iterations 1.1573767E-02 0.2654419 at 130iterations 6.7136800E-03 0.1425514 at 140iterations 3.8943752E-03 7.5738668E-02 at 150iterations 2.2622347E-03 4.6576500E-02 at 160iterations 1.3124181E-03 2.7820945E-02 at 170iterations 7.6394324E-04 1.5975952E-02 at 180iterations finished qdiffx linear iterations at : 03:24:24 total time elapsed so far: 11.81000 # loops : 180 mean,max change (kT/e) : 7.6394324E-04 1.5975952E-02 energy calculations done at 11.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.94000 DelPhi exited at 03:24:25 11.938u 0.213s 0:12.46 97.4% 0+0k 0+0io 0pf+0w