Mon Oct 10 14:13:57 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 Mon Oct 10 2011 at 14:13:57 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2742 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: 0.6248465 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): -11.71700 45.13300 ymin,ymax (A): -10.29600 46.67800 zmin,zma (A): -27.76000 20.09800 x,y,z range (A): 56.85000 56.97400 47.85800 scale (grids/A): 0.6248465 object centre (A): 16.70800 18.19100 -3.831000 number of atom coordinates read : 2742 total number of charged atoms : 2568 net assigned charge : 8.500025 assigned positive charge : 417.5126 centred at (gu) : 89.72644 90.27769 91.22391 assigned negative charge : -409.0133 centred at (gu) : 89.68909 90.20998 91.16228 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7204 nv = 96 ne = 84 npr = 54327 no. pairs analyzed = 54327 no. exposed pairs = 3574 no. arc points = 26048 no. surface atoms = 1184 nbur = 1558 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 385 mr = 3772 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2506 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8689 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2611499E-09 1.6657481E-08 midg,1,midg; midg,igrid,midg 2.2368918E-09 1.4070399E-08 1,midg,midg; igrid,midg,midg 5.1014251E-09 1.0219694E-08 gauss-seidel spectral radius is 0.9867518 estimated iterations to convergence 71 setup time was (sec) 0.6500000 now iterating at: 14:13:58 rms-change max change #iterations 0.1381476 24.72127 at 10iterations 1.2760925E-02 1.835720 at 20iterations 1.1916355E-03 0.1741600 at 30iterations 1.1188505E-04 1.5689850E-02 at 40iterations 1.1016764E-05 1.5559196E-03 at 50iterations finished qdiffx linear iterations at : 14:14:02 total time elapsed so far: 4.720000 # loops : 50 mean,max change (kT/e) : 1.1016764E-05 1.5559196E-03 energy calculations done at 4.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.900000 DelPhi exited at 14:14:03 4.909u 0.403s 0:05.85 90.5% 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 14:14:03 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2742 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: 1.874539 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): -11.71700 45.13300 ymin,ymax (A): -10.29600 46.67800 zmin,zma (A): -27.76000 20.09800 x,y,z range (A): 56.85000 56.97400 47.85800 scale (grids/A): 1.874539 object centre (A): 16.70800 18.19100 -3.831000 number of atom coordinates read : 2742 total number of charged atoms : 2568 net assigned charge : 8.500025 assigned positive charge : 417.5126 centred at (gu) : 89.17874 90.83237 93.67118 assigned negative charge : -409.0133 centred at (gu) : 89.06691 90.62965 93.48664 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26048 grid for indexing accessible points = 1.400000 m= 27201 mr = 52860 m= 4116 mr = 19332 m= 246 mr = 2409 m= 5 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 259 time to turn everything in is 0.6500000 number of dielectric boundary points 34870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20131 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) : 0.6248465 object centre at (A) : 16.70800 18.19100 -3.831000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9703736E-03 3.0943120E-02 midg,1,midg; midg,igrid,midg 8.3046593E-04 4.9984507E-02 1,midg,midg; igrid,midg,midg 1.4910568E-02 5.6098262E-03 gauss-seidel spectral radius is 0.9986078 estimated iterations to convergence 212 setup time was (sec) 0.9600000 now iterating at: 14:14:04 rms-change max change #iterations 4.290283 200.5811 at 10iterations 1.989966 68.33534 at 20iterations 0.9222863 30.00825 at 30iterations 0.4293221 13.58697 at 40iterations 0.1983168 6.761433 at 50iterations 9.2403986E-02 2.667834 at 60iterations 4.2798046E-02 1.525024 at 70iterations 1.9907938E-02 0.6269474 at 80iterations 9.2192991E-03 0.2868719 at 90iterations 4.2884024E-03 0.1477261 at 100iterations 1.9961151E-03 6.3874245E-02 at 110iterations 9.2535204E-04 3.1288147E-02 at 120iterations finished qdiffx linear iterations at : 14:14:14 total time elapsed so far: 11.04000 # loops : 120 mean,max change (kT/e) : 9.2535204E-04 3.1288147E-02 energy calculations done at 11.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.21000 DelPhi exited at 14:14:15 11.216u 0.473s 0:12.40 94.1% 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 14:14:15 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2742 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.811809 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): -11.71700 45.13300 ymin,ymax (A): -10.29600 46.67800 zmin,zma (A): -27.76000 20.09800 x,y,z range (A): 56.85000 56.97400 47.85800 scale (grids/A): 2.811809 object centre (A): 16.70800 18.19100 -3.831000 number of atom coordinates read : 2742 total number of charged atoms : 2568 net assigned charge : 8.500025 assigned positive charge : 417.5126 centred at (gu) : 88.76801 91.24846 95.50662 assigned negative charge : -409.0133 centred at (gu) : 88.60029 90.94431 95.23006 start vw surface at 0.1100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 180234 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26048 grid for indexing accessible points = 1.400000 m= 88893 mr = 128377 m= 30567 mr = 71214 m= 7308 mr = 23824 m= 1086 mr = 5284 m= 61 mr = 694 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 800 time to turn everything in is 1.680000 number of dielectric boundary points 78744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 20542 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) : 1.874539 object centre at (A) : 16.70800 18.19100 -3.831000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2800811E-02 0.2998371 midg,1,midg; midg,igrid,midg 1.6745344E-02 0.6601016 1,midg,midg; igrid,midg,midg 0.1136154 -0.2323693 gauss-seidel spectral radius is 0.9992549 estimated iterations to convergence 289 setup time was (sec) 2.050000 now iterating at: 14:14:18 rms-change max change #iterations 10.18633 380.2447 at 10iterations 5.998220 137.4651 at 20iterations 3.492094 69.46571 at 30iterations 2.027300 43.15167 at 40iterations 1.176936 24.56606 at 50iterations 0.6800577 13.01432 at 60iterations 0.3930464 7.572775 at 70iterations 0.2260807 4.256882 at 80iterations 0.1299136 2.638222 at 90iterations 7.4811108E-02 1.482552 at 100iterations 4.2910703E-02 0.7480774 at 110iterations 2.4676116E-02 0.4429302 at 120iterations 1.4167884E-02 0.2651901 at 130iterations 8.1293928E-03 0.1601181 at 140iterations 4.6662251E-03 8.8960648E-02 at 150iterations 2.6782302E-03 4.9751282E-02 at 160iterations 1.5352054E-03 2.7572632E-02 at 170iterations 8.8072481E-04 1.5783310E-02 at 180iterations finished qdiffx linear iterations at : 14:14:35 total time elapsed so far: 19.82000 # loops : 180 mean,max change (kT/e) : 8.8072481E-04 1.5783310E-02 energy calculations done at 19.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.99000 DelPhi exited at 14:14:36 19.997u 0.516s 0:20.91 98.0% 0+0k 0+0io 0pf+0w