Tue Oct 11 07:32:11 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 Tue Oct 11 2011 at 07:32:11 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3251 !!! WARNING: SEP 54 has a net charge of -0.4750 !!! WARNING: UMP 530 has a net charge of -0.1000 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: 0.5986714 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): 0.5549999 49.02400 ymin,ymax (A): -7.304000 49.50500 zmin,zma (A): 1.439000 60.90400 x,y,z range (A): 48.46900 56.80900 59.46500 scale (grids/A): 0.5986714 object centre (A): 24.78950 21.10050 31.17150 number of atom coordinates read : 3251 total number of charged atoms : 3103 net assigned charge : -1.574989 assigned positive charge : 490.4968 centred at (gu) : 89.64606 88.98893 90.76471 assigned negative charge : -492.0728 centred at (gu) : 89.55277 88.91969 90.67738 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7702 nv = 96 ne = 84 npr = 67081 no. pairs analyzed = 67081 no. exposed pairs = 3768 no. arc points = 25549 no. surface atoms = 1282 nbur = 1969 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 378 mr = 4546 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 0.3300000 number of dielectric boundary points 3486 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2644 ## 273 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9750 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8046624E-09 3.8426333E-09 midg,1,midg; midg,igrid,midg -4.6951207E-09 1.9134530E-09 1,midg,midg; igrid,midg,midg -5.2113460E-09 3.1937573E-09 gauss-seidel spectral radius is 0.9856082 estimated iterations to convergence 68 setup time was (sec) 0.5300000 now iterating at: 07:32:11 rms-change max change #iterations 0.1221739 17.34061 at 10iterations 1.1019945E-02 1.673965 at 20iterations 1.6920047E-03 0.2712708 at 30iterations 5.3785095E-04 9.2796326E-02 at 40iterations 1.9336073E-04 3.2951355E-02 at 50iterations finished qdiffx linear iterations at : 07:32:14 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 1.9336073E-04 3.2951355E-02 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 07:32:14 3.111u 0.162s 0:03.68 88.8% 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 Tue Oct 11 2011 at 07:32:14 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3251 !!! WARNING: SEP 54 has a net charge of -0.4750 !!! WARNING: UMP 530 has a net charge of -0.1000 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: 1.796014 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): 0.5549999 49.02400 ymin,ymax (A): -7.304000 49.50500 zmin,zma (A): 1.439000 60.90400 x,y,z range (A): 48.46900 56.80900 59.46500 scale (grids/A): 1.796014 object centre (A): 24.78950 21.10050 31.17150 number of atom coordinates read : 3251 total number of charged atoms : 3103 net assigned charge : -1.574989 assigned positive charge : 490.4968 centred at (gu) : 88.93741 86.96607 92.29314 assigned negative charge : -492.0728 centred at (gu) : 88.65799 86.75858 92.03200 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 84011 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25549 grid for indexing accessible points = 1.400000 m= 31207 mr = 60730 m= 4475 mr = 23939 m= 166 mr = 2904 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2107 time to turn everything in is 0.5500000 number of dielectric boundary points 32253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 209 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 24252 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) : 0.5986714 object centre at (A) : 24.78950 21.10050 31.17150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8215362E-02 8.5215457E-03 midg,1,midg; midg,igrid,midg -1.9772116E-02 4.6731215E-03 1,midg,midg; igrid,midg,midg -1.6005808E-02 1.5708961E-02 gauss-seidel spectral radius is 0.9985271 estimated iterations to convergence 207 setup time was (sec) 0.8300000 now iterating at: 07:32:15 rms-change max change #iterations 4.358912 174.5944 at 10iterations 1.994379 65.75095 at 20iterations 0.9087418 28.21137 at 30iterations 0.4150153 13.00896 at 40iterations 0.1892098 6.123299 at 50iterations 8.6514406E-02 2.606982 at 60iterations 3.9449893E-02 1.237144 at 70iterations 1.8154945E-02 0.5558662 at 80iterations 8.4672105E-03 0.2497139 at 90iterations 4.0632286E-03 0.1323144 at 100iterations 2.0550273E-03 7.1073532E-02 at 110iterations 1.1209256E-03 4.2984009E-02 at 120iterations finished qdiffx linear iterations at : 07:32:21 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 1.1209256E-03 4.2984009E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.980000 DelPhi exited at 07:32:22 6.980u 0.164s 0:07.89 90.4% 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 Tue Oct 11 2011 at 07:32:22 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3251 !!! WARNING: SEP 54 has a net charge of -0.4750 !!! WARNING: UMP 530 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.694021 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): 0.5549999 49.02400 ymin,ymax (A): -7.304000 49.50500 zmin,zma (A): 1.439000 60.90400 x,y,z range (A): 48.46900 56.80900 59.46500 scale (grids/A): 2.694021 object centre (A): 24.78950 21.10050 31.17150 number of atom coordinates read : 3251 total number of charged atoms : 3103 net assigned charge : -1.574989 assigned positive charge : 490.4968 centred at (gu) : 88.40593 85.44894 93.43944 assigned negative charge : -492.0728 centred at (gu) : 87.98672 85.13786 93.04781 start vw surface at 0.2000000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 194824 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25549 grid for indexing accessible points = 1.400000 m= 102255 mr = 146910 m= 36136 mr = 85855 m= 7860 mr = 29752 m= 857 mr = 6136 m= 22 mr = 528 m= 0 mr = 7 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 6877 time to turn everything in is 1.460000 number of dielectric boundary points 72766 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 24811 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) : 1.796014 object centre at (A) : 24.78950 21.10050 31.17150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3803681 1.4414849E-02 midg,1,midg; midg,igrid,midg -0.3241409 3.0741176E-02 1,midg,midg; igrid,midg,midg -0.1979460 0.2013295 gauss-seidel spectral radius is 0.9992364 estimated iterations to convergence 286 setup time was (sec) 1.740000 now iterating at: 07:32:24 rms-change max change #iterations 10.48551 325.0974 at 10iterations 6.081802 130.7672 at 20iterations 3.505769 73.98878 at 30iterations 2.008106 43.15892 at 40iterations 1.154261 22.11973 at 50iterations 0.6610396 12.52178 at 60iterations 0.3784833 6.897780 at 70iterations 0.2160573 4.198898 at 80iterations 0.1236660 2.360369 at 90iterations 7.0510365E-02 1.212395 at 100iterations 4.0281001E-02 0.7625659 at 110iterations 2.3093697E-02 0.4018021 at 120iterations 1.3354144E-02 0.2363443 at 130iterations 7.7711795E-03 0.1487055 at 140iterations 4.6194685E-03 9.1339111E-02 at 150iterations 2.8559037E-03 5.3985596E-02 at 160iterations 1.8631456E-03 3.6972046E-02 at 170iterations 1.2904936E-03 2.8228760E-02 at 180iterations finished qdiffx linear iterations at : 07:32:34 total time elapsed so far: 11.08000 # loops : 180 mean,max change (kT/e) : 1.2904936E-03 2.8228760E-02 energy calculations done at 11.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.26000 DelPhi exited at 07:32:34 11.264u 0.176s 0:11.85 96.4% 0+0k 0+0io 0pf+0w