Sat Oct 15 11:30:22 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 Sat Oct 15 2011 at 11:30:22 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 458 has a net charge of 1.4000 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: 0.6156187 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): -31.82300 17.49100 ymin,ymax (A): -23.23000 23.38400 zmin,zma (A): -12.55600 45.27200 x,y,z range (A): 49.31400 46.61400 57.82800 scale (grids/A): 0.6156187 object centre (A): -7.166000 7.6999664E-02 16.35800 number of atom coordinates read : 2585 total number of charged atoms : 2454 net assigned charge : 4.000010 assigned positive charge : 393.0041 centred at (gu) : 88.60023 88.98749 89.61056 assigned negative charge : -389.0045 centred at (gu) : 88.50893 89.03416 89.48854 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6331 nv = 96 ne = 84 npr = 53900 no. pairs analyzed = 53900 no. exposed pairs = 2991 no. arc points = 21838 no. surface atoms = 1003 nbur = 1582 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 353 mr = 3533 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.2000000 number of dielectric boundary points 3126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2142 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7946 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7435202E-09 9.1050465E-09 midg,1,midg; midg,igrid,midg 7.0189770E-09 1.5159353E-10 1,midg,midg; igrid,midg,midg -3.4931213E-09 6.0086793E-09 gauss-seidel spectral radius is 0.9863322 estimated iterations to convergence 70 setup time was (sec) 0.4200000 now iterating at: 11:30:22 rms-change max change #iterations 0.1224079 22.53917 at 10iterations 1.1057338E-02 1.709688 at 20iterations 1.0365603E-03 0.1469345 at 30iterations 9.6799624E-05 1.5375137E-02 at 40iterations 9.4361712E-06 1.4743805E-03 at 50iterations finished qdiffx linear iterations at : 11:30:26 total time elapsed so far: 3.800000 # loops : 50 mean,max change (kT/e) : 9.4361712E-06 1.4743805E-03 energy calculations done at 3.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 11:30:26 3.938u 0.249s 0:04.62 90.2% 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 Sat Oct 15 2011 at 11:30:26 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 458 has a net charge of 1.4000 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: 1.846856 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): -31.82300 17.49100 ymin,ymax (A): -23.23000 23.38400 zmin,zma (A): -12.55600 45.27200 x,y,z range (A): 49.31400 46.61400 57.82800 scale (grids/A): 1.846856 object centre (A): -7.166000 7.6999664E-02 16.35800 number of atom coordinates read : 2585 total number of charged atoms : 2454 net assigned charge : 4.000010 assigned positive charge : 393.0041 centred at (gu) : 85.80023 86.96207 88.83141 assigned negative charge : -389.0045 centred at (gu) : 85.52664 87.10225 88.46548 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21838 grid for indexing accessible points = 1.400000 m= 23610 mr = 48409 m= 3213 mr = 17376 m= 138 mr = 1868 m= 0 mr = 30 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 3861 time to turn everything in is 0.3700000 number of dielectric boundary points 28699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 19269 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) : 0.6156187 object centre at (A) : -7.166000 7.6999664E-02 16.35800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9394094E-02 2.1508988E-02 midg,1,midg; midg,igrid,midg 1.3999778E-02 1.8064780E-04 1,midg,midg; igrid,midg,midg -7.0386863E-04 2.8479027E-02 gauss-seidel spectral radius is 0.9985454 estimated iterations to convergence 208 setup time was (sec) 0.6300000 now iterating at: 11:30:27 rms-change max change #iterations 4.006675 171.0256 at 10iterations 1.834263 58.13121 at 20iterations 0.8342974 30.29403 at 30iterations 0.3821590 13.42732 at 40iterations 0.1746282 5.844606 at 50iterations 7.9744190E-02 2.797267 at 60iterations 3.6513060E-02 1.202433 at 70iterations 1.6708542E-02 0.5883369 at 80iterations 7.6466505E-03 0.2545681 at 90iterations 3.4882387E-03 0.1259518 at 100iterations 1.5927040E-03 4.8099518E-02 at 110iterations 7.3207426E-04 2.6329041E-02 at 120iterations finished qdiffx linear iterations at : 11:30:38 total time elapsed so far: 9.020000 # loops : 120 mean,max change (kT/e) : 7.3207426E-04 2.6329041E-02 energy calculations done at 9.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.160000 DelPhi exited at 11:30:38 9.160u 0.282s 0:12.23 77.1% 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 Sat Oct 15 2011 at 11:30:39 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 458 has a net charge of 1.4000 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: 2.770284 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): -31.82300 17.49100 ymin,ymax (A): -23.23000 23.38400 zmin,zma (A): -12.55600 45.27200 x,y,z range (A): 49.31400 46.61400 57.82800 scale (grids/A): 2.770284 object centre (A): -7.166000 7.6999664E-02 16.35800 number of atom coordinates read : 2585 total number of charged atoms : 2454 net assigned charge : 4.000010 assigned positive charge : 393.0041 centred at (gu) : 83.70020 85.44320 88.24683 assigned negative charge : -389.0045 centred at (gu) : 83.28983 85.65341 87.69817 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 160725 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21838 grid for indexing accessible points = 1.400000 m= 78277 mr = 117158 m= 25932 mr = 64162 m= 5623 mr = 20676 m= 595 mr = 4109 m= 24 mr = 333 m= 0 mr = 6 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 12984 time to turn everything in is 0.9500000 number of dielectric boundary points 64732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 19631 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) : 1.846856 object centre at (A) : -7.166000 7.6999664E-02 16.35800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1031797 0.2290471 midg,1,midg; midg,igrid,midg 0.1600468 -1.6819160E-02 1,midg,midg; igrid,midg,midg -1.8212878E-03 0.3796362 gauss-seidel spectral radius is 0.9992282 estimated iterations to convergence 284 setup time was (sec) 1.270000 now iterating at: 11:30:40 rms-change max change #iterations 9.426395 349.7134 at 10iterations 5.425339 133.0729 at 20iterations 3.087118 91.38641 at 30iterations 1.762007 44.01029 at 40iterations 1.004255 22.64207 at 50iterations 0.5711917 12.03452 at 60iterations 0.3250863 7.318338 at 70iterations 0.1843779 3.679245 at 80iterations 0.1044518 2.115490 at 90iterations 5.9354682E-02 1.161160 at 100iterations 3.3816371E-02 0.6303329 at 110iterations 1.9176753E-02 0.3780098 at 120iterations 1.0886414E-02 0.1932716 at 130iterations 6.1849463E-03 0.1248131 at 140iterations 3.5051494E-03 7.3505402E-02 at 150iterations 1.9939926E-03 3.8854599E-02 at 160iterations 1.1331087E-03 2.1499634E-02 at 170iterations 6.4348296E-04 1.2790680E-02 at 180iterations finished qdiffx linear iterations at : 11:30:55 total time elapsed so far: 15.18000 # loops : 180 mean,max change (kT/e) : 6.4348296E-04 1.2790680E-02 energy calculations done at 15.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.32000 DelPhi exited at 11:30:55 15.317u 0.350s 0:16.77 93.3% 0+0k 0+0io 0pf+0w