Tue Oct 11 05:11:45 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 Tue Oct 11 2011 at 05:11:45 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 = 2013 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: 0.7155203 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): -18.97400 23.88300 ymin,ymax (A): -10.34200 28.67400 zmin,zma (A): -2.165000 47.58900 x,y,z range (A): 42.85700 39.01600 49.75400 scale (grids/A): 0.7155203 object centre (A): 2.454500 9.166000 22.71200 number of atom coordinates read : 2013 total number of charged atoms : 1913 net assigned charge : 6.500009 assigned positive charge : 309.1790 centred at (gu) : 89.78501 89.14273 90.20605 assigned negative charge : -302.6792 centred at (gu) : 89.66461 89.17410 90.25977 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7137 nv = 96 ne = 84 npr = 39677 no. pairs analyzed = 39677 no. exposed pairs = 2468 no. arc points = 16832 no. surface atoms = 840 nbur = 1173 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4141 m= 2 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2800000 number of dielectric boundary points 3362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1571 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7767 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3244999E-08 3.6686771E-08 midg,1,midg; midg,igrid,midg 9.9111766E-08 4.1372239E-08 1,midg,midg; igrid,midg,midg -3.8262638E-09 1.2908994E-07 gauss-seidel spectral radius is 0.9898107 estimated iterations to convergence 81 setup time was (sec) 0.5700000 now iterating at: 05:11:46 rms-change max change #iterations 0.2101400 30.30357 at 10iterations 2.6276907E-02 4.340065 at 20iterations 3.4777389E-03 0.5220151 at 30iterations 4.9481605E-04 6.1508179E-02 at 40iterations 9.4805189E-05 1.2931824E-02 at 50iterations finished qdiffx linear iterations at : 05:11:50 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 9.4805189E-05 1.2931824E-02 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 05:11:50 3.999u 0.264s 0:05.02 84.6% 0+0k 0+0io 4pf+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 Tue Oct 11 2011 at 05:11:50 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 = 2013 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: 2.146561 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): -18.97400 23.88300 ymin,ymax (A): -10.34200 28.67400 zmin,zma (A): -2.165000 47.58900 x,y,z range (A): 42.85700 39.01600 49.75400 scale (grids/A): 2.146561 object centre (A): 2.454500 9.166000 22.71200 number of atom coordinates read : 2013 total number of charged atoms : 1913 net assigned charge : 6.500009 assigned positive charge : 309.1790 centred at (gu) : 89.35494 87.42818 90.61815 assigned negative charge : -302.6792 centred at (gu) : 88.99387 87.52251 90.77959 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 75064 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16832 grid for indexing accessible points = 1.400000 m= 31205 mr = 53471 m= 6419 mr = 24155 m= 653 mr = 4429 m= 18 mr = 361 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 378 time to turn everything in is 0.7000000 number of dielectric boundary points 30944 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 15197 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) : 0.7155203 object centre at (A) : 2.454500 9.166000 22.71200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1542128E-02 5.2984435E-02 midg,1,midg; midg,igrid,midg 3.9554145E-02 5.8281808E-03 1,midg,midg; igrid,midg,midg 2.4111144E-02 3.0077131E-02 gauss-seidel spectral radius is 0.9988481 estimated iterations to convergence 233 setup time was (sec) 1.000000 now iterating at: 05:11:52 rms-change max change #iterations 4.636614 175.8278 at 10iterations 2.313855 71.28563 at 20iterations 1.159056 34.90355 at 30iterations 0.5779529 22.29030 at 40iterations 0.2891352 8.648626 at 50iterations 0.1443808 4.258117 at 60iterations 7.2212473E-02 2.284767 at 70iterations 3.5945114E-02 1.096498 at 80iterations 1.7953364E-02 0.6581054 at 90iterations 9.0060979E-03 0.2626572 at 100iterations 4.5217252E-03 0.1457863 at 110iterations 2.2896372E-03 7.0808411E-02 at 120iterations finished qdiffx linear iterations at : 05:12:00 total time elapsed so far: 9.240000 # loops : 120 mean,max change (kT/e) : 2.2896372E-03 7.0808411E-02 energy calculations done at 9.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.410000 DelPhi exited at 05:12:01 9.416u 0.286s 0:10.34 93.7% 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 Tue Oct 11 2011 at 05:12:01 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 = 2013 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: 3.219841 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): -18.97400 23.88300 ymin,ymax (A): -10.34200 28.67400 zmin,zma (A): -2.165000 47.58900 x,y,z range (A): 42.85700 39.01600 49.75400 scale (grids/A): 3.219841 object centre (A): 2.454500 9.166000 22.71200 number of atom coordinates read : 2013 total number of charged atoms : 1913 net assigned charge : 6.500009 assigned positive charge : 309.1790 centred at (gu) : 89.03255 86.14221 90.92724 assigned negative charge : -302.6792 centred at (gu) : 88.49080 86.28379 91.16940 start vw surface at 0.1400000 fill in re-entrant regions at 0.9700000 boundary points on vw surface= 172787 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16832 grid for indexing accessible points = 1.400000 m= 96021 mr = 128569 m= 40730 mr = 80606 m= 12242 mr = 33975 m= 2677 mr = 9685 m= 343 mr = 2048 m= 9 mr = 236 m= 0 mr = 4 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 1260 time to turn everything in is 2.230000 number of dielectric boundary points 69686 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.370000 number of grid points assigned charge 15304 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) : 2.146561 object centre at (A) : 2.454500 9.166000 22.71200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3069440 0.6196423 midg,1,midg; midg,igrid,midg 0.2960235 2.8141366E-02 1,midg,midg; igrid,midg,midg 0.4078926 0.2439616 gauss-seidel spectral radius is 0.9992985 estimated iterations to convergence 298 setup time was (sec) 2.540000 now iterating at: 05:12:04 rms-change max change #iterations 10.22366 275.4756 at 10iterations 6.052849 135.2133 at 20iterations 3.574270 75.19170 at 30iterations 2.110298 40.71608 at 40iterations 1.246087 28.33623 at 50iterations 0.7314377 13.97157 at 60iterations 0.4299306 8.763887 at 70iterations 0.2525681 4.455394 at 80iterations 0.1484898 2.973045 at 90iterations 8.7241717E-02 1.663910 at 100iterations 5.1149987E-02 0.8434677 at 110iterations 3.0119330E-02 0.5119133 at 120iterations 1.7831827E-02 0.3051682 at 130iterations 1.0681397E-02 0.1962345 at 140iterations 6.5228520E-03 0.1174192 at 150iterations 4.1084690E-03 7.4512482E-02 at 160iterations 2.7173704E-03 4.7523499E-02 at 170iterations 1.9055724E-03 3.2554626E-02 at 180iterations finished qdiffx linear iterations at : 05:12:17 total time elapsed so far: 16.07000 # loops : 180 mean,max change (kT/e) : 1.9055724E-03 3.2554626E-02 energy calculations done at 16.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.25000 DelPhi exited at 05:12:18 16.256u 0.301s 0:16.83 98.3% 0+0k 0+0io 0pf+0w