Tue Nov 22 14:12:09 PST 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 Tue Nov 22 2011 at 14:12:10 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 0.5720162 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): -26.21300 36.02300 ymin,ymax (A): -18.95800 20.45800 zmin,zma (A): -3.242000 38.73900 x,y,z range (A): 62.23600 39.41600 41.98100 scale (grids/A): 0.5720162 object centre (A): 4.905002 0.7500000 17.74850 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 90.00563 90.29375 90.44966 assigned negative charge : -288.0263 centred at (gu) : 90.02802 90.37318 90.56396 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4255 nv = 96 ne = 84 npr = 39955 no. pairs analyzed = 39955 no. exposed pairs = 2472 no. arc points = 17445 no. surface atoms = 835 nbur = 1125 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 181 mr = 2282 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1819 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5384 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5596838E-09 -8.4969515E-10 midg,1,midg; midg,igrid,midg 1.2720710E-09 -3.9894799E-10 1,midg,midg; igrid,midg,midg 7.4790713E-10 2.6055713E-10 gauss-seidel spectral radius is 0.9841451 estimated iterations to convergence 65 setup time was (sec) 0.4400000 now iterating at: 14:12:11 rms-change max change #iterations 7.3131874E-02 15.95725 at 10iterations 5.4558879E-03 1.169337 at 20iterations 4.1449079E-04 0.1025696 at 30iterations 3.0592229E-05 6.0343742E-03 at 40iterations 2.2603724E-06 4.6730042E-04 at 50iterations finished qdiffx linear iterations at : 14:12:18 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 2.2603724E-06 4.6730042E-04 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 14:12:19 3.213u 0.235s 0:09.37 36.7% 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 Nov 22 2011 at 14:12:20 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 1.716049 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): -26.21300 36.02300 ymin,ymax (A): -18.95800 20.45800 zmin,zma (A): -3.242000 38.73900 x,y,z range (A): 62.23600 39.41600 41.98100 scale (grids/A): 1.716049 object centre (A): 4.905002 0.7500000 17.74850 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 90.01689 90.88124 91.34914 assigned negative charge : -288.0263 centred at (gu) : 90.08421 91.11968 91.69220 start vw surface at 0.1300000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 46542 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17445 grid for indexing accessible points = 1.400000 m= 15412 mr = 31513 m= 1605 mr = 11303 m= 55 mr = 890 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 763 time to turn everything in is 0.3600000 number of dielectric boundary points 19896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 225 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 14135 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) : 0.5720162 object centre at (A) : 4.905002 0.7500000 17.74850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6365533E-03 -4.3914448E-03 midg,1,midg; midg,igrid,midg 2.4767455E-03 -1.1211608E-03 1,midg,midg; igrid,midg,midg 3.0584520E-02 1.9336993E-02 gauss-seidel spectral radius is 0.9982410 estimated iterations to convergence 189 setup time was (sec) 0.6300000 now iterating at: 14:12:22 rms-change max change #iterations 2.917752 172.8483 at 10iterations 1.226301 54.46577 at 20iterations 0.5164074 22.07071 at 30iterations 0.2186787 8.660892 at 40iterations 9.2416674E-02 3.714043 at 50iterations 3.8993102E-02 1.602488 at 60iterations 1.6431674E-02 0.7487316 at 70iterations 6.9679595E-03 0.2707281 at 80iterations 2.9389597E-03 0.1344395 at 90iterations 1.2456800E-03 5.5547714E-02 at 100iterations 5.2384578E-04 2.3059845E-02 at 110iterations 2.2223653E-04 9.8609924E-03 at 120iterations finished qdiffx linear iterations at : 14:12:37 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 2.2223653E-04 9.8609924E-03 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.110000 DelPhi exited at 14:12:40 7.109u 0.227s 0:20.63 35.4% 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 Nov 22 2011 at 14:12:41 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 2.574073 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): -26.21300 36.02300 ymin,ymax (A): -18.95800 20.45800 zmin,zma (A): -3.242000 38.73900 x,y,z range (A): 62.23600 39.41600 41.98100 scale (grids/A): 2.574073 object centre (A): 4.905002 0.7500000 17.74850 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 90.02538 91.32192 92.02369 assigned negative charge : -288.0263 centred at (gu) : 90.12637 91.67957 92.53836 start vw surface at 0.1100000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 107642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17445 grid for indexing accessible points = 1.400000 m= 52381 mr = 76334 m= 15904 mr = 42719 m= 2495 mr = 12757 m= 193 mr = 1751 m= 2 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 2481 time to turn everything in is 0.7700000 number of dielectric boundary points 44952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 14620 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) : 1.716049 object centre at (A) : 4.905002 0.7500000 17.74850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7932176E-02 -4.5957536E-02 midg,1,midg; midg,igrid,midg 2.2126002E-02 -1.4486992E-02 1,midg,midg; igrid,midg,midg 0.3871226 0.2249115 gauss-seidel spectral radius is 0.9991237 estimated iterations to convergence 267 setup time was (sec) 1.030000 now iterating at: 14:12:48 rms-change max change #iterations 7.220423 272.5459 at 10iterations 3.980065 128.6048 at 20iterations 2.182333 61.85674 at 30iterations 1.195952 29.98149 at 40iterations 0.6524423 16.06810 at 50iterations 0.3558423 7.989366 at 60iterations 0.1945683 4.944193 at 70iterations 0.1059553 2.546892 at 80iterations 5.7715151E-02 1.479137 at 90iterations 3.1497169E-02 0.7514687 at 100iterations 1.7170118E-02 0.4236698 at 110iterations 9.3536908E-03 0.2370266 at 120iterations 5.0906707E-03 0.1277726 at 130iterations 2.7851723E-03 7.6170921E-02 at 140iterations 1.5143323E-03 3.4568787E-02 at 150iterations 8.2696357E-04 1.9716859E-02 at 160iterations 4.5089409E-04 1.0009766E-02 at 170iterations 2.4576718E-04 6.0665607E-03 at 180iterations finished qdiffx linear iterations at : 14:13:16 total time elapsed so far: 10.09000 # loops : 180 mean,max change (kT/e) : 2.4576718E-04 6.0665607E-03 energy calculations done at 10.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.27000 DelPhi exited at 14:13:18 10.274u 0.154s 0:37.00 28.1% 0+0k 0+0io 0pf+0w