Tue Oct 11 06:16:06 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 06:16:06 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 = 2014 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7299869 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): -19.89400 24.18300 ymin,ymax (A): -11.11400 28.62200 zmin,zma (A): -2.690000 46.07800 x,y,z range (A): 44.07700 39.73600 48.76800 scale (grids/A): 0.7299869 object centre (A): 2.144501 8.754000 21.69400 number of atom coordinates read : 2014 total number of charged atoms : 1890 net assigned charge : 6.500006 assigned positive charge : 304.6401 centred at (gu) : 90.00565 89.37366 91.00600 assigned negative charge : -298.1402 centred at (gu) : 89.84828 89.40933 91.09635 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7419 nv = 96 ne = 84 npr = 40306 no. pairs analyzed = 40306 no. exposed pairs = 2424 no. arc points = 16754 no. surface atoms = 834 nbur = 1180 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 557 mr = 4330 m= 10 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3525 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1548 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7970 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3382905E-07 2.6095943E-08 midg,1,midg; midg,igrid,midg 1.3472865E-07 5.8260721E-08 1,midg,midg; igrid,midg,midg -3.0167577E-08 2.1193028E-07 gauss-seidel spectral radius is 0.9902074 estimated iterations to convergence 82 setup time was (sec) 0.6700000 now iterating at: 06:16:07 rms-change max change #iterations 0.2264205 31.70221 at 10iterations 2.9797107E-02 3.831531 at 20iterations 4.0507573E-03 0.6156235 at 30iterations 6.2588585E-04 8.2015991E-02 at 40iterations 1.3236288E-04 1.7112732E-02 at 50iterations finished qdiffx linear iterations at : 06:16:11 total time elapsed so far: 4.510000 # loops : 50 mean,max change (kT/e) : 1.3236288E-04 1.7112732E-02 energy calculations done at 4.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.750000 DelPhi exited at 06:16:11 4.750u 0.443s 0:05.71 90.8% 0+0k 0+0io 6pf+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 06:16:11 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 = 2014 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.189961 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): -19.89400 24.18300 ymin,ymax (A): -11.11400 28.62200 zmin,zma (A): -2.690000 46.07800 x,y,z range (A): 44.07700 39.73600 48.76800 scale (grids/A): 2.189961 object centre (A): 2.144501 8.754000 21.69400 number of atom coordinates read : 2014 total number of charged atoms : 1890 net assigned charge : 6.500006 assigned positive charge : 304.6401 centred at (gu) : 90.01717 88.12116 93.01800 assigned negative charge : -298.1402 centred at (gu) : 89.54485 88.22791 93.28914 start vw surface at 0.1300000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 77610 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16754 grid for indexing accessible points = 1.400000 m= 33434 mr = 55358 m= 7634 mr = 26010 m= 853 mr = 5416 m= 32 mr = 508 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8300000 number of dielectric boundary points 32264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 15026 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) : 0.7299869 object centre at (A) : 2.144501 8.754000 21.69400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9341986E-02 1.1571563E-02 midg,1,midg; midg,igrid,midg 4.1935869E-02 8.2228361E-03 1,midg,midg; igrid,midg,midg 2.3919005E-02 5.4837648E-02 gauss-seidel spectral radius is 0.9988859 estimated iterations to convergence 237 setup time was (sec) 1.250000 now iterating at: 06:16:13 rms-change max change #iterations 4.768679 192.4299 at 10iterations 2.395455 74.22392 at 20iterations 1.213651 35.63393 at 30iterations 0.6130837 18.14414 at 40iterations 0.3095123 9.709684 at 50iterations 0.1569578 4.613743 at 60iterations 7.9139926E-02 2.321934 at 70iterations 4.0124077E-02 1.194322 at 80iterations 2.0244952E-02 0.5993462 at 90iterations 1.0302451E-02 0.3107709 at 100iterations 5.2409852E-03 0.1628952 at 110iterations 2.6970732E-03 9.1499329E-02 at 120iterations finished qdiffx linear iterations at : 06:16:23 total time elapsed so far: 11.26000 # loops : 120 mean,max change (kT/e) : 2.6970732E-03 9.1499329E-02 energy calculations done at 11.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.47000 DelPhi exited at 06:16:24 11.478u 0.508s 0:12.51 95.6% 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 Tue Oct 11 2011 at 06:16:24 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 = 2014 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.284941 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): -19.89400 24.18300 ymin,ymax (A): -11.11400 28.62200 zmin,zma (A): -2.690000 46.07800 x,y,z range (A): 44.07700 39.73600 48.76800 scale (grids/A): 3.284941 object centre (A): 2.144501 8.754000 21.69400 number of atom coordinates read : 2014 total number of charged atoms : 1890 net assigned charge : 6.500006 assigned positive charge : 304.6401 centred at (gu) : 90.02565 87.18162 94.52695 assigned negative charge : -298.1402 centred at (gu) : 89.31746 87.34196 94.93368 start vw surface at 0.1500000 fill in re-entrant regions at 1.030000 boundary points on vw surface= 178543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16754 grid for indexing accessible points = 1.400000 m= 101232 mr = 132855 m= 45162 mr = 85348 m= 14940 mr = 37976 m= 3433 mr = 12026 m= 493 mr = 2622 m= 22 mr = 329 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 1.430000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.610000 number of dielectric boundary points 72665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.800000 number of grid points assigned charge 15118 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) : 2.189961 object centre at (A) : 2.144501 8.754000 21.69400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2522147 3.0428590E-02 midg,1,midg; midg,igrid,midg 0.3369186 3.9206129E-02 1,midg,midg; igrid,midg,midg 0.3507691 0.4381378 gauss-seidel spectral radius is 0.9993073 estimated iterations to convergence 300 setup time was (sec) 3.010000 now iterating at: 06:16:28 rms-change max change #iterations 10.47297 416.3111 at 10iterations 6.242436 137.2594 at 20iterations 3.716744 76.47154 at 30iterations 2.203440 42.95313 at 40iterations 1.308703 22.44749 at 50iterations 0.7715771 14.53191 at 60iterations 0.4553785 7.845253 at 70iterations 0.2691193 4.548622 at 80iterations 0.1588363 2.699969 at 90iterations 9.3719698E-02 1.754620 at 100iterations 5.5155557E-02 0.9549789 at 110iterations 3.2621633E-02 0.6433693 at 120iterations 1.9393116E-02 0.3421249 at 130iterations 1.1585055E-02 0.2101021 at 140iterations 7.0939623E-03 0.1220813 at 150iterations 4.4683032E-03 8.8126183E-02 at 160iterations 2.9422785E-03 5.4687500E-02 at 170iterations 2.0657727E-03 3.6514282E-02 at 180iterations finished qdiffx linear iterations at : 06:16:44 total time elapsed so far: 19.74000 # loops : 180 mean,max change (kT/e) : 2.0657727E-03 3.6514282E-02 energy calculations done at 19.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.97000 DelPhi exited at 06:16:45 19.979u 0.486s 0:20.74 98.6% 0+0k 0+0io 0pf+0w