Sat Oct 15 14:36:24 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 Sat Oct 15 2011 at 14:36:24 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2824 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.6186570 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): -8.828000 48.71600 ymin,ymax (A): -7.772000 39.05400 zmin,zma (A): -0.1980000 57.19400 x,y,z range (A): 57.54400 46.82600 57.39200 scale (grids/A): 0.6186570 object centre (A): 19.94400 15.64100 28.49800 number of atom coordinates read : 2824 total number of charged atoms : 2683 net assigned charge : -0.4859670 assigned positive charge : 427.5762 centred at (gu) : 89.11504 89.61758 88.41288 assigned negative charge : -428.0632 centred at (gu) : 89.01325 89.49768 88.40125 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7342 nv = 96 ne = 84 npr = 55970 no. pairs analyzed = 55970 no. exposed pairs = 3739 no. arc points = 26474 no. surface atoms = 1263 nbur = 1561 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3807 m= 4 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.2100000 number of dielectric boundary points 3884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2671 ## 277 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8920 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5124930E-09 3.9735676E-10 midg,1,midg; midg,igrid,midg -9.5684030E-09 7.4004607E-09 1,midg,midg; igrid,midg,midg -9.1278993E-09 5.5957612E-09 gauss-seidel spectral radius is 0.9864975 estimated iterations to convergence 70 setup time was (sec) 0.4800000 now iterating at: 14:36:27 rms-change max change #iterations 0.1290572 18.14797 at 10iterations 1.1923427E-02 2.026581 at 20iterations 1.1040596E-03 0.1451340 at 30iterations 1.0056083E-04 1.6727448E-02 at 40iterations 1.0951880E-05 1.6212463E-03 at 50iterations finished qdiffx linear iterations at : 14:36:33 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 1.0951880E-05 1.6212463E-03 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 14:36:34 4.327u 0.308s 0:09.92 46.5% 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 Sat Oct 15 2011 at 14:36:34 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2824 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.855971 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): -8.828000 48.71600 ymin,ymax (A): -7.772000 39.05400 zmin,zma (A): -0.1980000 57.19400 x,y,z range (A): 57.54400 46.82600 57.39200 scale (grids/A): 1.855971 object centre (A): 19.94400 15.64100 28.49800 number of atom coordinates read : 2824 total number of charged atoms : 2683 net assigned charge : -0.4859670 assigned positive charge : 427.5762 centred at (gu) : 87.34435 88.85182 85.23798 assigned negative charge : -428.0632 centred at (gu) : 87.03944 88.49266 85.20350 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79147 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26474 grid for indexing accessible points = 1.400000 m= 26505 mr = 53185 m= 3780 mr = 18755 m= 167 mr = 2131 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 704 time to turn everything in is 0.4100000 number of dielectric boundary points 35481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 216 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 21032 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) : 0.6186570 object centre at (A) : 19.94400 15.64100 28.49800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6193183E-02 2.2110414E-02 midg,1,midg; midg,igrid,midg -1.7347481E-02 1.2375641E-02 1,midg,midg; igrid,midg,midg -5.2482203E-02 2.6716067E-02 gauss-seidel spectral radius is 0.9985927 estimated iterations to convergence 211 setup time was (sec) 0.6600000 now iterating at: 14:36:35 rms-change max change #iterations 4.270278 186.8463 at 10iterations 1.967785 68.04494 at 20iterations 0.9060588 27.70480 at 30iterations 0.4194808 13.09281 at 40iterations 0.1943423 5.735321 at 50iterations 8.9627013E-02 2.826516 at 60iterations 4.1542463E-02 1.404261 at 70iterations 1.9174922E-02 0.5985661 at 80iterations 8.8641690E-03 0.2678375 at 90iterations 4.1056187E-03 0.1289883 at 100iterations 1.8961667E-03 5.6747437E-02 at 110iterations 8.7816728E-04 2.7240753E-02 at 120iterations finished qdiffx linear iterations at : 14:36:43 total time elapsed so far: 8.840000 # loops : 120 mean,max change (kT/e) : 8.7816728E-04 2.7240753E-02 energy calculations done at 8.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.970000 DelPhi exited at 14:36:44 8.968u 0.288s 0:09.85 93.8% 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 Sat Oct 15 2011 at 14:36:44 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2824 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.783957 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): -8.828000 48.71600 ymin,ymax (A): -7.772000 39.05400 zmin,zma (A): -0.1980000 57.19400 x,y,z range (A): 57.54400 46.82600 57.39200 scale (grids/A): 2.783957 object centre (A): 19.94400 15.64100 28.49800 number of atom coordinates read : 2824 total number of charged atoms : 2683 net assigned charge : -0.4859670 assigned positive charge : 427.5762 centred at (gu) : 86.01640 88.27752 82.85667 assigned negative charge : -428.0632 centred at (gu) : 85.55901 87.73895 82.80515 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 183263 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26474 grid for indexing accessible points = 1.400000 m= 87842 mr = 130002 m= 29664 mr = 69939 m= 6410 mr = 22975 m= 752 mr = 4534 m= 24 mr = 448 m= 0 mr = 4 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 2261 time to turn everything in is 1.040000 number of dielectric boundary points 80053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 21461 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) : 1.855971 object centre at (A) : 19.94400 15.64100 28.49800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3114351 0.5799668 midg,1,midg; midg,igrid,midg -0.1574631 0.1157825 1,midg,midg; igrid,midg,midg -0.6753609 0.3258483 gauss-seidel spectral radius is 0.9992679 estimated iterations to convergence 292 setup time was (sec) 1.330000 now iterating at: 14:36:45 rms-change max change #iterations 10.32993 315.8319 at 10iterations 6.145634 162.5492 at 20iterations 3.618499 95.47266 at 30iterations 2.113988 50.92314 at 40iterations 1.230309 26.22622 at 50iterations 0.7154954 14.26768 at 60iterations 0.4150878 8.097505 at 70iterations 0.2407541 4.740871 at 80iterations 0.1392065 2.354749 at 90iterations 8.0433279E-02 1.667675 at 100iterations 4.6418667E-02 0.8843434 at 110iterations 2.6789548E-02 0.5661974 at 120iterations 1.5476454E-02 0.3786449 at 130iterations 8.9245252E-03 0.1858766 at 140iterations 5.1480816E-03 9.8708153E-02 at 150iterations 2.9674536E-03 5.5433273E-02 at 160iterations 1.7097523E-03 3.2737732E-02 at 170iterations 9.8728808E-04 1.8410325E-02 at 180iterations finished qdiffx linear iterations at : 14:36:59 total time elapsed so far: 14.77000 # loops : 180 mean,max change (kT/e) : 9.8728808E-04 1.8410325E-02 energy calculations done at 14.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.89000 DelPhi exited at 14:37:00 14.894u 0.309s 0:15.89 95.5% 0+0k 0+0io 0pf+0w