Sun Oct 9 19:55:54 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 Sun Oct 9 2011 at 19:55:54 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5259 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5476165 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): 3.288000 68.29700 ymin,ymax (A): -8.978000 53.39800 zmin,zma (A): -1.163000 63.68200 x,y,z range (A): 65.00900 62.37600 64.84500 scale (grids/A): 0.5476165 object centre (A): 35.79250 22.21000 31.25950 number of atom coordinates read : 5259 total number of charged atoms : 5100 net assigned charge : 0.6350421 assigned positive charge : 809.1934 centred at (gu) : 87.97631 89.31396 89.09484 assigned negative charge : -808.5645 centred at (gu) : 87.83745 89.34949 89.01178 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 10252 nv = 96 ne = 84 npr = 107059 no. pairs analyzed = 107059 no. exposed pairs = 6123 no. arc points = 41743 no. surface atoms = 2088 nbur = 3171 mkacc time = 0.2800000 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 = 1.596000 m= 460 mr = 5875 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 4806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4219 ## 476 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 13515 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2314638E-09 9.0915486E-10 midg,1,midg; midg,igrid,midg 6.4398986E-10 -3.0640238E-10 1,midg,midg; igrid,midg,midg -2.8654079E-09 1.1094768E-09 gauss-seidel spectral radius is 0.9829699 estimated iterations to convergence 63 setup time was (sec) 0.9000000 now iterating at: 19:55:55 rms-change max change #iterations 0.1062567 13.20140 at 10iterations 9.4696581E-03 1.316879 at 20iterations 2.7573965E-03 0.3067322 at 30iterations 1.2674837E-03 0.1447520 at 40iterations 6.0601049E-04 7.4890614E-02 at 50iterations finished qdiffx linear iterations at : 19:56:00 total time elapsed so far: 5.440000 # loops : 50 mean,max change (kT/e) : 6.0601049E-04 7.4890614E-02 energy calculations done at 5.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.600000 DelPhi exited at 19:56:00 5.609u 0.464s 0:06.34 95.5% 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 Sun Oct 9 2011 at 19:56:00 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5259 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.642849 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): 3.288000 68.29700 ymin,ymax (A): -8.978000 53.39800 zmin,zma (A): -1.163000 63.68200 x,y,z range (A): 65.00900 62.37600 64.84500 scale (grids/A): 1.642849 object centre (A): 35.79250 22.21000 31.25950 number of atom coordinates read : 5259 total number of charged atoms : 5100 net assigned charge : 0.6350421 assigned positive charge : 809.1934 centred at (gu) : 83.92783 87.94041 87.28333 assigned negative charge : -808.5645 centred at (gu) : 83.51228 88.04825 87.03519 start vw surface at 0.1900000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 114888 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41743 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 39680 mr = 83466 m= 4701 mr = 28774 m= 135 mr = 2542 m= 0 mr = 17 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 44605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 392 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 39058 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) : 0.5476165 object centre at (A) : 35.79250 22.21000 31.25950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1396300E-02 1.6111536E-02 midg,1,midg; midg,igrid,midg 2.0285584E-02 8.6481702E-03 1,midg,midg; igrid,midg,midg -2.8783081E-02 1.4871495E-02 gauss-seidel spectral radius is 0.9984131 estimated iterations to convergence 199 setup time was (sec) 1.330000 now iterating at: 19:56:02 rms-change max change #iterations 4.840896 160.7494 at 10iterations 2.137076 68.44463 at 20iterations 0.9469748 26.39471 at 30iterations 0.4183264 11.77873 at 40iterations 0.1851503 5.010074 at 50iterations 8.2552694E-02 2.239291 at 60iterations 3.7043508E-02 1.047291 at 70iterations 1.7067801E-02 0.4501848 at 80iterations 8.3965221E-03 0.2420120 at 90iterations 4.6287077E-03 0.1444292 at 100iterations 2.9440157E-03 8.0031395E-02 at 110iterations 2.0884958E-03 5.4594040E-02 at 120iterations finished qdiffx linear iterations at : 19:56:15 total time elapsed so far: 14.28000 # loops : 120 mean,max change (kT/e) : 2.0884958E-03 5.4594040E-02 energy calculations done at 14.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.46000 DelPhi exited at 19:56:16 14.461u 0.522s 0:15.27 98.1% 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 Sun Oct 9 2011 at 19:56:16 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5259 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.464274 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): 3.288000 68.29700 ymin,ymax (A): -8.978000 53.39800 zmin,zma (A): -1.163000 63.68200 x,y,z range (A): 65.00900 62.37600 64.84500 scale (grids/A): 2.464274 object centre (A): 35.79250 22.21000 31.25950 number of atom coordinates read : 5259 total number of charged atoms : 5100 net assigned charge : 0.6350421 assigned positive charge : 809.1934 centred at (gu) : 80.89134 86.91028 85.92443 assigned negative charge : -808.5645 centred at (gu) : 80.26845 87.07231 85.55283 start vw surface at 0.1900000 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 267100 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41743 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 134387 mr = 202808 m= 42129 mr = 110002 m= 7643 mr = 32820 m= 588 mr = 5253 m= 10 mr = 330 m= 0 mr = 0 time to grow re-entrant surface = 1.580000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.480000 number of dielectric boundary points 100644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 2.660000 number of grid points assigned charge 40752 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) : 1.642849 object centre at (A) : 35.79250 22.21000 31.25950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4893441 0.3835472 midg,1,midg; midg,igrid,midg 0.1985125 5.6232773E-03 1,midg,midg; igrid,midg,midg -0.5378416 0.1573589 gauss-seidel spectral radius is 0.9992492 estimated iterations to convergence 288 setup time was (sec) 2.900000 now iterating at: 19:56:19 rms-change max change #iterations 12.28508 372.0876 at 10iterations 7.216609 144.6032 at 20iterations 4.217668 87.98385 at 30iterations 2.452959 49.90684 at 40iterations 1.421709 23.85127 at 50iterations 0.8232973 14.33685 at 60iterations 0.4752958 7.877815 at 70iterations 0.2736665 4.854323 at 80iterations 0.1576293 2.645155 at 90iterations 9.0860441E-02 1.504517 at 100iterations 5.2539371E-02 0.7897794 at 110iterations 3.0457836E-02 0.4929428 at 120iterations 1.7875591E-02 0.3070679 at 130iterations 1.0788985E-02 0.2123451 at 140iterations 6.7677614E-03 0.1334457 at 150iterations 4.5090746E-03 7.5282574E-02 at 160iterations 3.2486240E-03 5.5133820E-02 at 170iterations 2.5048775E-03 4.0470123E-02 at 180iterations finished qdiffx linear iterations at : 19:56:40 total time elapsed so far: 23.99000 # loops : 180 mean,max change (kT/e) : 2.5048775E-03 4.0470123E-02 energy calculations done at 23.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.16000 DelPhi exited at 19:56:41 24.160u 0.594s 0:25.00 99.0% 0+0k 0+0io 0pf+0w