Mon Oct 10 17:03:26 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 17:03:26 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 = 2754 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5591945 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): -13.87500 49.78800 ymin,ymax (A): -26.48400 18.14300 zmin,zma (A): -42.08800 5.454000 x,y,z range (A): 63.66300 44.62700 47.54200 scale (grids/A): 0.5591945 object centre (A): 17.95650 -4.170500 -18.31700 number of atom coordinates read : 2754 total number of charged atoms : 2614 net assigned charge : -0.4999678 assigned positive charge : 412.2423 centred at (gu) : 89.64105 89.63824 89.33174 assigned negative charge : -412.7434 centred at (gu) : 89.71494 89.50594 89.22477 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5691 nv = 96 ne = 84 npr = 54680 no. pairs analyzed = 54680 no. exposed pairs = 3711 no. arc points = 26383 no. surface atoms = 1247 nbur = 1507 mkacc time = 0.1300000 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 = 1.540000 m= 224 mr = 2797 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2676 ## 342 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7354 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3242627E-09 8.6184704E-10 midg,1,midg; midg,igrid,midg -1.5125943E-09 1.1540552E-09 1,midg,midg; igrid,midg,midg 7.5685347E-10 -7.1847406E-10 gauss-seidel spectral radius is 0.9834937 estimated iterations to convergence 64 setup time was (sec) 0.5500000 now iterating at: 17:03:27 rms-change max change #iterations 7.7727959E-02 12.88424 at 10iterations 5.5042207E-03 0.8403645 at 20iterations 3.8907881E-04 6.5158844E-02 at 30iterations 2.7872644E-05 4.8398972E-03 at 40iterations 2.0083271E-06 3.2901764E-04 at 50iterations finished qdiffx linear iterations at : 17:03:30 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 2.0083271E-06 3.2901764E-04 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 17:03:33 3.371u 0.158s 0:06.15 57.2% 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 17:03:33 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 = 2754 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.677583 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): -13.87500 49.78800 ymin,ymax (A): -26.48400 18.14300 zmin,zma (A): -42.08800 5.454000 x,y,z range (A): 63.66300 44.62700 47.54200 scale (grids/A): 1.677583 object centre (A): 17.95650 -4.170500 -18.31700 number of atom coordinates read : 2754 total number of charged atoms : 2614 net assigned charge : -0.4999678 assigned positive charge : 412.2423 centred at (gu) : 88.92238 88.91404 87.99445 assigned negative charge : -412.7434 centred at (gu) : 89.14461 88.51743 87.67402 start vw surface at 0.2400000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 62401 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26383 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18926 mr = 40830 m= 2004 mr = 12796 m= 71 mr = 886 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 513 time to turn everything in is 0.5700000 number of dielectric boundary points 28890 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 272 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 20132 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) : 0.5591945 object centre at (A) : 17.95650 -4.170500 -18.31700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3015703E-02 6.7854514E-03 midg,1,midg; midg,igrid,midg -4.9936925E-03 3.3487999E-03 1,midg,midg; igrid,midg,midg 1.5795334E-03 -5.1059644E-03 gauss-seidel spectral radius is 0.9982678 estimated iterations to convergence 191 setup time was (sec) 0.8400000 now iterating at: 17:03:34 rms-change max change #iterations 3.366965 171.9040 at 10iterations 1.423846 64.17706 at 20iterations 0.6069311 23.03473 at 30iterations 0.2572002 10.54801 at 40iterations 0.1096733 3.936264 at 50iterations 4.6690587E-02 1.714691 at 60iterations 1.9850897E-02 0.7620544 at 70iterations 8.4387567E-03 0.3380623 at 80iterations 3.5890548E-03 0.1327381 at 90iterations 1.5293062E-03 6.0138702E-02 at 100iterations 6.4913393E-04 2.3658752E-02 at 110iterations 2.7734175E-04 9.3278885E-03 at 120iterations finished qdiffx linear iterations at : 17:03:41 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 2.7734175E-04 9.3278885E-03 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 17:03:41 8.177u 0.178s 0:08.84 94.3% 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 17:03:42 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 = 2754 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.516375 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): -13.87500 49.78800 ymin,ymax (A): -26.48400 18.14300 zmin,zma (A): -42.08800 5.454000 x,y,z range (A): 63.66300 44.62700 47.54200 scale (grids/A): 2.516375 object centre (A): 17.95650 -4.170500 -18.31700 number of atom coordinates read : 2754 total number of charged atoms : 2614 net assigned charge : -0.4999678 assigned positive charge : 412.2423 centred at (gu) : 88.38337 88.37086 86.99141 assigned negative charge : -412.7434 centred at (gu) : 88.71686 87.77617 86.51101 start vw surface at 0.1600000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 144707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26383 grid for indexing accessible points = 1.400000 m= 64907 mr = 100203 m= 18872 mr = 50413 m= 3044 mr = 13951 m= 229 mr = 1855 m= 2 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 1801 time to turn everything in is 1.110000 number of dielectric boundary points 65250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 20895 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) : 1.677583 object centre at (A) : 17.95650 -4.170500 -18.31700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1826732 0.1054142 midg,1,midg; midg,igrid,midg -6.4207643E-02 2.6211038E-02 1,midg,midg; igrid,midg,midg 5.1716965E-02 0.3539433 gauss-seidel spectral radius is 0.9991674 estimated iterations to convergence 274 setup time was (sec) 1.410000 now iterating at: 17:03:44 rms-change max change #iterations 8.796764 387.5958 at 10iterations 5.007407 131.4109 at 20iterations 2.826900 81.91576 at 30iterations 1.593444 40.59100 at 40iterations 0.8954391 20.97620 at 50iterations 0.5006558 12.13347 at 60iterations 0.2794109 7.125984 at 70iterations 0.1556782 3.392994 at 80iterations 8.6610183E-02 1.870169 at 90iterations 4.8431437E-02 0.9546857 at 100iterations 2.6880529E-02 0.6469154 at 110iterations 1.4904018E-02 0.3080893 at 120iterations 8.2651740E-03 0.1560016 at 130iterations 4.6019549E-03 9.2659205E-02 at 140iterations 2.5505219E-03 5.4450989E-02 at 150iterations 1.4175136E-03 2.9075623E-02 at 160iterations 7.8477972E-04 1.5977859E-02 at 170iterations 4.3623644E-04 8.5487366E-03 at 180iterations finished qdiffx linear iterations at : 17:03:54 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 4.3623644E-04 8.5487366E-03 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.35000 DelPhi exited at 17:03:55 12.355u 0.210s 0:13.40 93.7% 0+0k 0+0io 0pf+0w