Sun Oct 9 16:39:29 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 Sun Oct 9 2011 at 16:39:29 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 = 2832 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: 0.6081001 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): 59.02200 116.8300 ymin,ymax (A): -27.05300 22.88800 zmin,zma (A): -18.16300 40.38000 x,y,z range (A): 57.80800 49.94100 58.54300 scale (grids/A): 0.6081001 object centre (A): 87.92600 -2.082500 11.10850 number of atom coordinates read : 2832 total number of charged atoms : 2700 net assigned charge : 0.5000077 assigned positive charge : 415.1114 centred at (gu) : 88.85979 89.81253 92.74870 assigned negative charge : -414.6126 centred at (gu) : 88.99618 89.87061 92.74545 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7094 nv = 96 ne = 84 npr = 55874 no. pairs analyzed = 55874 no. exposed pairs = 3832 no. arc points = 28032 no. surface atoms = 1296 nbur = 1536 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 366 mr = 3502 m= 5 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2100000 number of dielectric boundary points 3927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2787 ## 269 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8788 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6912560E-11 6.3397559E-10 midg,1,midg; midg,igrid,midg 3.1672627E-09 -2.5929487E-09 1,midg,midg; igrid,midg,midg 8.8602041E-09 -5.1420161E-09 gauss-seidel spectral radius is 0.9860345 estimated iterations to convergence 69 setup time was (sec) 0.4200000 now iterating at: 16:39:29 rms-change max change #iterations 0.1137646 20.63271 at 10iterations 1.0412946E-02 1.642868 at 20iterations 1.1551675E-03 0.1900368 at 30iterations 2.9499069E-04 4.3043137E-02 at 40iterations 1.0656679E-04 1.4446259E-02 at 50iterations finished qdiffx linear iterations at : 16:39:33 total time elapsed so far: 3.590000 # loops : 50 mean,max change (kT/e) : 1.0656679E-04 1.4446259E-02 energy calculations done at 3.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.720000 DelPhi exited at 16:39:33 3.725u 0.199s 0:04.23 92.4% 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 Sun Oct 9 2011 at 16:39:33 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 = 2832 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: 1.824300 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): 59.02200 116.8300 ymin,ymax (A): -27.05300 22.88800 zmin,zma (A): -18.16300 40.38000 x,y,z range (A): 57.80800 49.94100 58.54300 scale (grids/A): 1.824300 object centre (A): 87.92600 -2.082500 11.10850 number of atom coordinates read : 2832 total number of charged atoms : 2700 net assigned charge : 0.5000077 assigned positive charge : 415.1114 centred at (gu) : 86.57879 89.43689 98.24549 assigned negative charge : -414.6126 centred at (gu) : 86.98853 89.61166 98.23612 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76187 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28032 grid for indexing accessible points = 1.400000 m= 25004 mr = 49466 m= 3659 mr = 17288 m= 201 mr = 2083 m= 4 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 735 time to turn everything in is 0.3700000 number of dielectric boundary points 36141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 21092 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) : 0.6081001 object centre at (A) : 87.92600 -2.082500 11.10850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4674321E-03 -9.3356296E-03 midg,1,midg; midg,igrid,midg 3.0914471E-03 -1.4688700E-02 1,midg,midg; igrid,midg,midg 3.9103154E-02 -1.3172036E-02 gauss-seidel spectral radius is 0.9985561 estimated iterations to convergence 209 setup time was (sec) 0.6000000 now iterating at: 16:39:34 rms-change max change #iterations 4.063936 200.7887 at 10iterations 1.840690 72.35938 at 20iterations 0.8415518 28.16548 at 30iterations 0.3855456 13.05665 at 40iterations 0.1766902 5.974327 at 50iterations 8.0843069E-02 2.640888 at 60iterations 3.6996052E-02 1.318853 at 70iterations 1.6918803E-02 0.5442085 at 80iterations 7.8392290E-03 0.2564135 at 90iterations 3.6396843E-03 0.1277466 at 100iterations 1.7165615E-03 5.8086395E-02 at 110iterations 8.4144378E-04 2.8962135E-02 at 120iterations finished qdiffx linear iterations at : 16:39:42 total time elapsed so far: 8.450000 # loops : 120 mean,max change (kT/e) : 8.4144378E-04 2.8962135E-02 energy calculations done at 8.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.590000 DelPhi exited at 16:39:42 8.592u 0.239s 0:09.30 94.8% 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 Sun Oct 9 2011 at 16:39:42 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 = 2832 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: 2.736450 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): 59.02200 116.8300 ymin,ymax (A): -27.05300 22.88800 zmin,zma (A): -18.16300 40.38000 x,y,z range (A): 57.80800 49.94100 58.54300 scale (grids/A): 2.736450 object centre (A): 87.92600 -2.082500 11.10850 number of atom coordinates read : 2832 total number of charged atoms : 2700 net assigned charge : 0.5000077 assigned positive charge : 415.1114 centred at (gu) : 84.86794 89.15517 102.3681 assigned negative charge : -414.6126 centred at (gu) : 85.48273 89.41747 102.3540 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 176412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28032 grid for indexing accessible points = 1.400000 m= 81753 mr = 121197 m= 27868 mr = 64179 m= 6328 mr = 21275 m= 826 mr = 4533 m= 46 mr = 549 m= 0 mr = 10 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 2592 time to turn everything in is 0.9500000 number of dielectric boundary points 81490 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 21594 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) : 1.824300 object centre at (A) : 87.92600 -2.082500 11.10850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1997423 -0.2417342 midg,1,midg; midg,igrid,midg 6.9500148E-02 -0.2636084 1,midg,midg; igrid,midg,midg 0.8288188 -0.1826731 gauss-seidel spectral radius is 0.9992610 estimated iterations to convergence 290 setup time was (sec) 1.200000 now iterating at: 16:39:44 rms-change max change #iterations 9.778419 410.0091 at 10iterations 5.792471 161.1321 at 20iterations 3.399546 74.78990 at 30iterations 1.986642 40.44897 at 40iterations 1.152946 27.51701 at 50iterations 0.6691874 13.46484 at 60iterations 0.3879005 7.154013 at 70iterations 0.2238840 4.710481 at 80iterations 0.1296691 2.350921 at 90iterations 7.4721292E-02 1.418594 at 100iterations 4.3064039E-02 0.8127739 at 110iterations 2.4785755E-02 0.4773598 at 120iterations 1.4298093E-02 0.2618713 at 130iterations 8.2388576E-03 0.1614609 at 140iterations 4.7810497E-03 8.7068081E-02 at 150iterations 2.7796135E-03 5.5342674E-02 at 160iterations 1.6365735E-03 3.1399250E-02 at 170iterations 9.8374742E-04 1.9332886E-02 at 180iterations finished qdiffx linear iterations at : 16:39:57 total time elapsed so far: 13.79000 # loops : 180 mean,max change (kT/e) : 9.8374742E-04 1.9332886E-02 energy calculations done at 13.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.93000 DelPhi exited at 16:39:57 13.927u 0.315s 0:14.64 97.1% 0+0k 0+0io 0pf+0w