Mon Oct 10 09:43:33 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 09:43:33 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 = 2814 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: 0.5868003 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): -17.23800 36.02300 ymin,ymax (A): -64.26800 -4.753000 zmin,zma (A): -3.494000 57.17400 x,y,z range (A): 53.26100 59.51500 60.66800 scale (grids/A): 0.5868003 object centre (A): 9.392499 -34.51050 26.84000 number of atom coordinates read : 2814 total number of charged atoms : 2664 net assigned charge : 6.000015 assigned positive charge : 411.9000 centred at (gu) : 89.22976 89.13690 87.30627 assigned negative charge : -405.9004 centred at (gu) : 89.32034 89.04173 87.19399 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6445 nv = 96 ne = 84 npr = 55071 no. pairs analyzed = 55071 no. exposed pairs = 4293 no. arc points = 30893 no. surface atoms = 1418 nbur = 1396 mkacc time = 8.9999996E-02 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 = 1.484000 m= 350 mr = 2778 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 4007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3034 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8136 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1911220E-09 2.4279687E-09 midg,1,midg; midg,igrid,midg -8.2913221E-10 3.3372243E-09 1,midg,midg; igrid,midg,midg 4.7324420E-09 -4.4000695E-10 gauss-seidel spectral radius is 0.9850105 estimated iterations to convergence 67 setup time was (sec) 0.3500000 now iterating at: 09:43:33 rms-change max change #iterations 9.8957196E-02 16.61748 at 10iterations 7.9126060E-03 1.304443 at 20iterations 6.9799938E-04 0.1266880 at 30iterations 9.2995659E-05 2.3479462E-02 at 40iterations 2.0692740E-05 4.9343109E-03 at 50iterations finished qdiffx linear iterations at : 09:43:36 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.0692740E-05 4.9343109E-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) 3.370000 DelPhi exited at 09:43:37 3.378u 0.243s 0:03.99 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 Mon Oct 10 2011 at 09:43:37 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 = 2814 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: 1.760401 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): -17.23800 36.02300 ymin,ymax (A): -64.26800 -4.753000 zmin,zma (A): -3.494000 57.17400 x,y,z range (A): 53.26100 59.51500 60.66800 scale (grids/A): 1.760401 object centre (A): 9.392499 -34.51050 26.84000 number of atom coordinates read : 2814 total number of charged atoms : 2664 net assigned charge : 6.000015 assigned positive charge : 411.9000 centred at (gu) : 87.68903 87.41039 81.91818 assigned negative charge : -405.9004 centred at (gu) : 87.96068 87.12476 81.58197 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 68924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30893 grid for indexing accessible points = 1.400000 m= 21496 mr = 41675 m= 2737 mr = 13294 m= 122 mr = 1182 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 79 time to turn everything in is 0.3600000 number of dielectric boundary points 37114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 272 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 20777 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) : 0.5868003 object centre at (A) : 9.392499 -34.51050 26.84000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0783257E-03 7.3047928E-03 midg,1,midg; midg,igrid,midg 2.4842527E-02 3.7044544E-02 1,midg,midg; igrid,midg,midg 1.6426755E-02 4.3203076E-03 gauss-seidel spectral radius is 0.9984459 estimated iterations to convergence 201 setup time was (sec) 0.5900000 now iterating at: 09:43:37 rms-change max change #iterations 3.713927 199.3827 at 10iterations 1.648349 69.30950 at 20iterations 0.7281581 25.75206 at 30iterations 0.3227128 13.02768 at 40iterations 0.1431317 4.875142 at 50iterations 6.3808896E-02 2.475655 at 60iterations 2.8243147E-02 0.9690526 at 70iterations 1.2554884E-02 0.4413376 at 80iterations 5.5878605E-03 0.2182503 at 90iterations 2.4784827E-03 8.5843086E-02 at 100iterations 1.1027917E-03 3.8080215E-02 at 110iterations 4.9171527E-04 1.7497063E-02 at 120iterations finished qdiffx linear iterations at : 09:43:45 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 4.9171527E-04 1.7497063E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 09:43:45 7.871u 0.180s 0:08.33 96.6% 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 09:43:45 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 = 2814 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: 2.640601 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): -17.23800 36.02300 ymin,ymax (A): -64.26800 -4.753000 zmin,zma (A): -3.494000 57.17400 x,y,z range (A): 53.26100 59.51500 60.66800 scale (grids/A): 2.640601 object centre (A): 9.392499 -34.51050 26.84000 number of atom coordinates read : 2814 total number of charged atoms : 2664 net assigned charge : 6.000015 assigned positive charge : 411.9000 centred at (gu) : 86.53341 86.11535 77.87734 assigned negative charge : -405.9004 centred at (gu) : 86.94083 85.68717 77.37296 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 159095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30893 grid for indexing accessible points = 1.400000 m= 70481 mr = 102871 m= 22668 mr = 51817 m= 4367 mr = 15907 m= 377 mr = 2490 m= 5 mr = 124 m= 0 mr = 2 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 235 time to turn everything in is 0.8700000 number of dielectric boundary points 83782 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 21304 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) : 1.760401 object centre at (A) : 9.392499 -34.51050 26.84000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1061835 0.1017538 midg,1,midg; midg,igrid,midg 0.6857753 0.5023300 1,midg,midg; igrid,midg,midg 0.1429168 0.1053842 gauss-seidel spectral radius is 0.9992339 estimated iterations to convergence 285 setup time was (sec) 1.130000 now iterating at: 09:43:46 rms-change max change #iterations 9.492385 313.8305 at 10iterations 5.637145 152.7677 at 20iterations 3.296466 112.3932 at 30iterations 1.913691 52.43517 at 40iterations 1.108569 28.19347 at 50iterations 0.6378193 17.00140 at 60iterations 0.3659360 9.562235 at 70iterations 0.2099400 5.046488 at 80iterations 0.1202415 2.795556 at 90iterations 6.8770163E-02 1.463953 at 100iterations 3.9234832E-02 0.8352364 at 110iterations 2.2415876E-02 0.5331659 at 120iterations 1.2789411E-02 0.2534313 at 130iterations 7.3017841E-03 0.1600189 at 140iterations 4.1590077E-03 8.4890842E-02 at 150iterations 2.3669768E-03 4.9309731E-02 at 160iterations 1.3513626E-03 3.2238960E-02 at 170iterations 7.7372656E-04 1.5123367E-02 at 180iterations finished qdiffx linear iterations at : 09:43:58 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 7.7372656E-04 1.5123367E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 09:43:58 12.755u 0.193s 0:13.28 97.4% 0+0k 0+0io 0pf+0w