Sat Oct 8 11:32:32 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 Sat Oct 8 2011 at 11:32:32 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2534 !!! WARNING: HIY 389 has a net charge of 0.2000 !!! WARNING: HIZ 405 has a net charge of 0.2000 !!! WARNING: HIZ 409 has a net charge of 0.2000 !!! WARNING: HIZ 415 has a net charge of 0.2000 !!! WARNING: ZN7 749 has a net charge of 1.4000 !!! WARNING: ZN7 750 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6691729 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): -16.34600 31.83900 ymin,ymax (A): 38.36600 82.12300 zmin,zma (A): 56.53200 109.7320 x,y,z range (A): 48.18500 43.75700 53.20000 scale (grids/A): 0.6691729 object centre (A): 7.746500 60.24450 83.13200 number of atom coordinates read : 2534 total number of charged atoms : 2392 net assigned charge : 1.100004 assigned positive charge : 388.5170 centred at (gu) : 91.13312 91.58371 89.31068 assigned negative charge : -387.4175 centred at (gu) : 90.98635 91.65472 89.41556 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7390 nv = 96 ne = 84 npr = 52704 no. pairs analyzed = 52704 no. exposed pairs = 3010 no. arc points = 21376 no. surface atoms = 1019 nbur = 1515 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4109 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.3000000 number of dielectric boundary points 3680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2076 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8838 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3479665E-08 -1.9927171E-08 midg,1,midg; midg,igrid,midg 1.4973619E-08 -2.0365118E-08 1,midg,midg; igrid,midg,midg -2.6578741E-08 4.9609920E-08 gauss-seidel spectral radius is 0.9884126 estimated iterations to convergence 76 setup time was (sec) 0.5100000 now iterating at: 11:32:32 rms-change max change #iterations 0.1853081 27.27274 at 10iterations 1.9876983E-02 3.240521 at 20iterations 2.2017153E-03 0.3116550 at 30iterations 2.4235142E-04 2.9047012E-02 at 40iterations 2.6421414E-05 3.3721924E-03 at 50iterations finished qdiffx linear iterations at : 11:32:35 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 2.6421414E-05 3.3721924E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 11:32:35 3.138u 0.159s 0:03.62 90.6% 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 8 2011 at 11:32:35 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2534 !!! WARNING: HIY 389 has a net charge of 0.2000 !!! WARNING: HIZ 405 has a net charge of 0.2000 !!! WARNING: HIZ 409 has a net charge of 0.2000 !!! WARNING: HIZ 415 has a net charge of 0.2000 !!! WARNING: ZN7 749 has a net charge of 1.4000 !!! WARNING: ZN7 750 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.007519 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): -16.34600 31.83900 ymin,ymax (A): 38.36600 82.12300 zmin,zma (A): 56.53200 109.7320 x,y,z range (A): 48.18500 43.75700 53.20000 scale (grids/A): 2.007519 object centre (A): 7.746500 60.24450 83.13200 number of atom coordinates read : 2534 total number of charged atoms : 2392 net assigned charge : 1.100004 assigned positive charge : 388.5170 centred at (gu) : 93.39900 94.75063 87.93146 assigned negative charge : -387.4175 centred at (gu) : 92.95892 94.96386 88.24670 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 79565 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21376 grid for indexing accessible points = 1.400000 m= 29048 mr = 55348 m= 5242 mr = 21494 m= 458 mr = 3440 m= 9 mr = 202 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 414 time to turn everything in is 0.5700000 number of dielectric boundary points 33839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 18925 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) : 0.6691729 object centre at (A) : 7.746500 60.24450 83.13200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6467531E-02 -2.7249457E-02 midg,1,midg; midg,igrid,midg 7.6200869E-03 -2.0630671E-02 1,midg,midg; igrid,midg,midg -1.1621549E-02 2.0963054E-02 gauss-seidel spectral radius is 0.9987507 estimated iterations to convergence 224 setup time was (sec) 0.8500000 now iterating at: 11:32:36 rms-change max change #iterations 4.729678 198.5653 at 10iterations 2.276703 82.08911 at 20iterations 1.100354 33.26994 at 30iterations 0.5328931 16.00667 at 40iterations 0.2575823 7.503717 at 50iterations 0.1243864 3.934461 at 60iterations 6.0151961E-02 1.689641 at 70iterations 2.9198539E-02 0.8204670 at 80iterations 1.4104828E-02 0.4138820 at 90iterations 6.8296012E-03 0.2018299 at 100iterations 3.3021877E-03 0.1029549 at 110iterations 1.5976094E-03 4.9540043E-02 at 120iterations finished qdiffx linear iterations at : 11:32:43 total time elapsed so far: 7.000000 # loops : 120 mean,max change (kT/e) : 1.5976094E-03 4.9540043E-02 energy calculations done at 7.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.170000 DelPhi exited at 11:32:43 7.170u 0.162s 0:07.71 95.0% 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 Sat Oct 8 2011 at 11:32:43 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2534 !!! WARNING: HIY 389 has a net charge of 0.2000 !!! WARNING: HIZ 405 has a net charge of 0.2000 !!! WARNING: HIZ 409 has a net charge of 0.2000 !!! WARNING: HIZ 415 has a net charge of 0.2000 !!! WARNING: ZN7 749 has a net charge of 1.4000 !!! WARNING: ZN7 750 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.011278 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): -16.34600 31.83900 ymin,ymax (A): 38.36600 82.12300 zmin,zma (A): 56.53200 109.7320 x,y,z range (A): 48.18500 43.75700 53.20000 scale (grids/A): 3.011278 object centre (A): 7.746500 60.24450 83.13200 number of atom coordinates read : 2534 total number of charged atoms : 2392 net assigned charge : 1.100004 assigned positive charge : 388.5170 centred at (gu) : 95.09838 97.12585 86.89698 assigned negative charge : -387.4175 centred at (gu) : 94.43837 97.44585 87.37000 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 183676 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21376 grid for indexing accessible points = 1.400000 m= 93135 mr = 133985 m= 35569 mr = 76197 m= 9751 mr = 28707 m= 1835 mr = 7533 m= 174 mr = 1333 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 1418 time to turn everything in is 1.400000 number of dielectric boundary points 76315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 19135 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) : 2.007519 object centre at (A) : 7.746500 60.24450 83.13200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9268282 -0.1905976 midg,1,midg; midg,igrid,midg 4.5020901E-02 -0.4196962 1,midg,midg; igrid,midg,midg -8.5589081E-02 9.8548554E-02 gauss-seidel spectral radius is 0.9992841 estimated iterations to convergence 295 setup time was (sec) 1.670000 now iterating at: 11:32:45 rms-change max change #iterations 10.73707 427.2035 at 10iterations 6.279512 132.8968 at 20iterations 3.653925 66.06133 at 30iterations 2.132593 36.12167 at 40iterations 1.240992 20.76525 at 50iterations 0.7203147 13.18985 at 60iterations 0.4181556 8.212982 at 70iterations 0.2424094 3.911671 at 80iterations 0.1404237 2.357582 at 90iterations 8.1563480E-02 1.375157 at 100iterations 4.7238283E-02 0.8173561 at 110iterations 2.7365301E-02 0.5102222 at 120iterations 1.5869638E-02 0.2515678 at 130iterations 9.2159854E-03 0.1611506 at 140iterations 5.3238305E-03 9.0984344E-02 at 150iterations 3.0844014E-03 5.2310944E-02 at 160iterations 1.7894296E-03 2.8713226E-02 at 170iterations 1.0377450E-03 1.7372131E-02 at 180iterations finished qdiffx linear iterations at : 11:32:54 total time elapsed so far: 11.11000 # loops : 180 mean,max change (kT/e) : 1.0377450E-03 1.7372131E-02 energy calculations done at 11.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.29000 DelPhi exited at 11:32:55 11.294u 0.199s 0:11.80 97.2% 0+0k 0+0io 0pf+0w