Mon Oct 10 09:12:17 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 09:12:17 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6534388 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): -5.581000 34.25500 ymin,ymax (A): -3.352000 49.14400 zmin,zma (A): -23.66200 30.81900 x,y,z range (A): 39.83600 52.49600 54.48100 scale (grids/A): 0.6534388 object centre (A): 14.33700 22.89600 3.578501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.70248 92.36755 90.04862 assigned negative charge : -284.8263 centred at (gu) : 90.80346 92.48375 89.98203 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5697 nv = 96 ne = 84 npr = 40527 no. pairs analyzed = 40527 no. exposed pairs = 2503 no. arc points = 17632 no. surface atoms = 849 nbur = 1115 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 293 mr = 3161 m= 0 mr = 26 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.1600000 number of dielectric boundary points 2803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1800 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6760 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3175548E-09 1.5014749E-08 midg,1,midg; midg,igrid,midg 1.2713421E-08 -1.2842735E-08 1,midg,midg; igrid,midg,midg 1.6377220E-08 -6.5694454E-09 gauss-seidel spectral radius is 0.9878066 estimated iterations to convergence 74 setup time was (sec) 0.3600000 now iterating at: 09:12:17 rms-change max change #iterations 0.1337521 19.65882 at 10iterations 1.3990467E-02 1.971834 at 20iterations 1.4299181E-03 0.2194138 at 30iterations 1.4829336E-04 2.1530151E-02 at 40iterations 1.5418227E-05 2.3956299E-03 at 50iterations finished qdiffx linear iterations at : 09:12:20 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.5418227E-05 2.3956299E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 09:12:21 3.400u 0.159s 0:03.82 92.9% 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 09:12:21 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.960316 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): -5.581000 34.25500 ymin,ymax (A): -3.352000 49.14400 zmin,zma (A): -23.66200 30.81900 x,y,z range (A): 39.83600 52.49600 54.48100 scale (grids/A): 1.960316 object centre (A): 14.33700 22.89600 3.578501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 92.10735 97.10262 90.14595 assigned negative charge : -284.8263 centred at (gu) : 92.41072 97.45164 89.94621 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 60984 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17632 grid for indexing accessible points = 1.400000 m= 22019 mr = 41628 m= 3355 mr = 16628 m= 158 mr = 2190 m= 0 mr = 54 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1955 time to turn everything in is 0.3100000 number of dielectric boundary points 26016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 14453 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) : 0.6534388 object centre at (A) : 14.33700 22.89600 3.578501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8055101E-02 1.4331580E-02 midg,1,midg; midg,igrid,midg 3.5123479E-02 -1.3975881E-02 1,midg,midg; igrid,midg,midg 6.7444909E-03 -4.7159623E-03 gauss-seidel spectral radius is 0.9986337 estimated iterations to convergence 214 setup time was (sec) 0.5200000 now iterating at: 09:12:22 rms-change max change #iterations 3.758488 168.1095 at 10iterations 1.764442 59.14287 at 20iterations 0.8256949 29.57883 at 30iterations 0.3865576 12.99059 at 40iterations 0.1802832 6.536474 at 50iterations 8.4436096E-02 3.028811 at 60iterations 3.9439775E-02 1.449228 at 70iterations 1.8430645E-02 0.6132784 at 80iterations 8.5936049E-03 0.2809448 at 90iterations 4.0293271E-03 0.1424422 at 100iterations 1.8892884E-03 6.9520295E-02 at 110iterations 8.8250422E-04 3.1805038E-02 at 120iterations finished qdiffx linear iterations at : 09:12:29 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 8.8250422E-04 3.1805038E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 09:12:29 7.769u 0.214s 0:08.23 96.8% 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 Mon Oct 10 2011 at 09:12:29 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.940475 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): -5.581000 34.25500 ymin,ymax (A): -3.352000 49.14400 zmin,zma (A): -23.66200 30.81900 x,y,z range (A): 39.83600 52.49600 54.48100 scale (grids/A): 2.940475 object centre (A): 14.33700 22.89600 3.578501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 93.16113 100.6540 90.21899 assigned negative charge : -284.8263 centred at (gu) : 93.61608 101.1775 89.91918 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 140911 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17632 grid for indexing accessible points = 1.400000 m= 70933 mr = 100762 m= 25819 mr = 58504 m= 5940 mr = 21357 m= 746 mr = 4548 m= 40 mr = 506 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 6772 time to turn everything in is 0.8000000 number of dielectric boundary points 58696 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 14655 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) : 1.960316 object centre at (A) : 14.33700 22.89600 3.578501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9724311 1.6335653E-02 midg,1,midg; midg,igrid,midg 0.3359428 -0.1744215 1,midg,midg; igrid,midg,midg 3.7276823E-02 -2.6084436E-02 gauss-seidel spectral radius is 0.9992477 estimated iterations to convergence 288 setup time was (sec) 1.020000 now iterating at: 09:12:30 rms-change max change #iterations 8.761345 468.8116 at 10iterations 5.028173 122.2771 at 20iterations 2.873435 62.30529 at 30iterations 1.640945 32.55748 at 40iterations 0.9390976 20.65854 at 50iterations 0.5357881 11.01443 at 60iterations 0.3048449 6.585621 at 70iterations 0.1741754 3.361984 at 80iterations 9.9233709E-02 2.121735 at 90iterations 5.6554176E-02 1.084452 at 100iterations 3.2237269E-02 0.5838316 at 110iterations 1.8441932E-02 0.3907290 at 120iterations 1.0508208E-02 0.1947556 at 130iterations 6.0001924E-03 0.1133232 at 140iterations 3.4254971E-03 7.3410034E-02 at 150iterations 1.9526100E-03 3.5316467E-02 at 160iterations 1.1120202E-03 2.5829315E-02 at 170iterations 6.3416897E-04 1.1796474E-02 at 180iterations finished qdiffx linear iterations at : 09:12:41 total time elapsed so far: 12.16000 # loops : 180 mean,max change (kT/e) : 6.3416897E-04 1.1796474E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 09:12:42 12.291u 0.221s 0:12.77 97.9% 0+0k 0+0io 0pf+0w