Mon Oct 10 09:22:01 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 Mon Oct 10 2011 at 09:22:01 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 = 3033 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5766583 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): 112.3140 174.0490 ymin,ymax (A): -44.00900 10.35500 zmin,zma (A): 47.61200 104.9440 x,y,z range (A): 61.73500 54.36400 57.33200 scale (grids/A): 0.5766583 object centre (A): 143.1815 -16.82700 76.27800 number of atom coordinates read : 3033 total number of charged atoms : 2879 net assigned charge : 5.000019 assigned positive charge : 444.5216 centred at (gu) : 89.78664 89.60506 89.69439 assigned negative charge : -439.5222 centred at (gu) : 89.76746 89.67735 89.56688 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6834 nv = 96 ne = 84 npr = 58401 no. pairs analyzed = 58401 no. exposed pairs = 4663 no. arc points = 33949 no. surface atoms = 1530 nbur = 1503 mkacc time = 9.9999994E-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= 407 mr = 2948 m= 3 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3276 ## 343 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8590 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6663917E-09 3.1864389E-09 midg,1,midg; midg,igrid,midg 2.6056028E-09 -3.9891537E-10 1,midg,midg; igrid,midg,midg 6.3239947E-10 1.2857370E-09 gauss-seidel spectral radius is 0.9845080 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 09:22:01 rms-change max change #iterations 9.6368656E-02 14.94347 at 10iterations 7.2423294E-03 1.208836 at 20iterations 5.5472984E-04 8.1409454E-02 at 30iterations 4.6032656E-05 8.0223083E-03 at 40iterations 4.9746131E-06 6.8473816E-04 at 50iterations finished qdiffx linear iterations at : 09:22:04 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 4.9746131E-06 6.8473816E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 09:22:05 3.478u 0.164s 0:03.91 92.8% 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 Mon Oct 10 2011 at 09:22:05 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 = 3033 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: 1.729975 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): 112.3140 174.0490 ymin,ymax (A): -44.00900 10.35500 zmin,zma (A): 47.61200 104.9440 x,y,z range (A): 61.73500 54.36400 57.33200 scale (grids/A): 1.729975 object centre (A): 143.1815 -16.82700 76.27800 number of atom coordinates read : 3033 total number of charged atoms : 2879 net assigned charge : 5.000019 assigned positive charge : 444.5216 centred at (gu) : 89.35951 88.81437 89.08279 assigned negative charge : -439.5222 centred at (gu) : 89.30193 89.03169 88.70040 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72609 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33949 grid for indexing accessible points = 1.400000 m= 24391 mr = 43793 m= 3746 mr = 15505 m= 146 mr = 1886 m= 3 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 69 time to turn everything in is 0.3700000 number of dielectric boundary points 39692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 272 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 22291 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) : 0.5766583 object centre at (A) : 143.1815 -16.82700 76.27800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7213902E-02 3.3489451E-02 midg,1,midg; midg,igrid,midg 1.8679760E-02 9.4627859E-03 1,midg,midg; igrid,midg,midg 7.2410831E-04 1.0781694E-02 gauss-seidel spectral radius is 0.9984278 estimated iterations to convergence 200 setup time was (sec) 0.6000000 now iterating at: 09:22:05 rms-change max change #iterations 3.766884 192.4233 at 10iterations 1.657516 62.27733 at 20iterations 0.7269726 25.94629 at 30iterations 0.3215721 10.85664 at 40iterations 0.1419402 4.991546 at 50iterations 6.2558614E-02 2.181604 at 60iterations 2.7637932E-02 0.9004059 at 70iterations 1.2207526E-02 0.4269505 at 80iterations 5.4026432E-03 0.1819859 at 90iterations 2.3852482E-03 9.9045634E-02 at 100iterations 1.0534029E-03 3.7252426E-02 at 110iterations 4.6718790E-04 1.6399384E-02 at 120iterations finished qdiffx linear iterations at : 09:22:13 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 4.6718790E-04 1.6399384E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 09:22:13 7.954u 0.205s 0:08.73 93.3% 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 Mon Oct 10 2011 at 09:22:13 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 = 3033 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.594962 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): 112.3140 174.0490 ymin,ymax (A): -44.00900 10.35500 zmin,zma (A): 47.61200 104.9440 x,y,z range (A): 61.73500 54.36400 57.33200 scale (grids/A): 2.594962 object centre (A): 143.1815 -16.82700 76.27800 number of atom coordinates read : 3033 total number of charged atoms : 2879 net assigned charge : 5.000019 assigned positive charge : 444.5216 centred at (gu) : 89.03883 88.22135 88.62390 assigned negative charge : -439.5222 centred at (gu) : 88.95282 88.54742 88.05058 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 167790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33949 grid for indexing accessible points = 1.400000 m= 77470 mr = 108591 m= 27852 mr = 57202 m= 6250 mr = 20138 m= 631 mr = 4098 m= 18 mr = 289 m= 0 mr = 2 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 207 time to turn everything in is 0.9400000 number of dielectric boundary points 89691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 23018 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) : 1.729975 object centre at (A) : 143.1815 -16.82700 76.27800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1920259 0.4897071 midg,1,midg; midg,igrid,midg 0.2297802 0.1373922 1,midg,midg; igrid,midg,midg 5.6503724E-02 3.5389565E-02 gauss-seidel spectral radius is 0.9992369 estimated iterations to convergence 286 setup time was (sec) 1.190000 now iterating at: 09:22:15 rms-change max change #iterations 9.641982 320.4385 at 10iterations 5.705268 129.7412 at 20iterations 3.338916 81.59594 at 30iterations 1.936565 44.64611 at 40iterations 1.121017 24.39132 at 50iterations 0.6452441 13.18858 at 60iterations 0.3706524 8.027822 at 70iterations 0.2125327 4.797515 at 80iterations 0.1216615 2.496259 at 90iterations 6.9432870E-02 1.816570 at 100iterations 3.9638698E-02 0.8157873 at 110iterations 2.2680808E-02 0.4641495 at 120iterations 1.2914323E-02 0.2618656 at 130iterations 7.3624533E-03 0.1457443 at 140iterations 4.1997093E-03 8.7402344E-02 at 150iterations 2.3901451E-03 4.9652100E-02 at 160iterations 1.3633168E-03 2.7389526E-02 at 170iterations 7.7498693E-04 1.6906738E-02 at 180iterations finished qdiffx linear iterations at : 09:22:26 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 7.7498693E-04 1.6906738E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 09:22:27 12.896u 0.188s 0:13.35 97.9% 0+0k 0+0io 0pf+0w