Mon Oct 10 13:53:21 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 13:53:22 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4406 !!! WARNING: HIT 442 has a net charge of 0.5140 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: 0.5027894 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): -3.495000 67.31000 ymin,ymax (A): -12.61800 38.32500 zmin,zma (A): -19.70400 45.31700 x,y,z range (A): 70.80500 50.94300 65.02100 scale (grids/A): 0.5027894 object centre (A): 31.90750 12.85350 12.80650 number of atom coordinates read : 4406 total number of charged atoms : 4251 net assigned charge : -5.485952 assigned positive charge : 667.0689 centred at (gu) : 88.10113 89.91595 90.78999 assigned negative charge : -672.5572 centred at (gu) : 88.15556 90.02272 90.80912 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6893 nv = 96 ne = 84 npr = 92574 no. pairs analyzed = 92574 no. exposed pairs = 5054 no. arc points = 33675 no. surface atoms = 1732 nbur = 2674 mkacc time = 0.1600000 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 = 1.680000 m= 242 mr = 3849 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3395 ## 516 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 9365 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9068400E-11 -1.1021487E-10 midg,1,midg; midg,igrid,midg 1.2907773E-10 -2.3831889E-10 1,midg,midg; igrid,midg,midg 6.5093417E-11 -9.1492092E-11 gauss-seidel spectral radius is 0.9797359 estimated iterations to convergence 58 setup time was (sec) 0.4900000 now iterating at: 13:53:22 rms-change max change #iterations 5.9912790E-02 10.02041 at 10iterations 3.7873783E-03 0.5898204 at 20iterations 6.1119907E-04 9.3212128E-02 at 30iterations 1.7244632E-04 2.7297974E-02 at 40iterations 5.0953833E-05 8.2130432E-03 at 50iterations finished qdiffx linear iterations at : 13:53:25 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 5.0953833E-05 8.2130432E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 13:53:27 3.554u 0.183s 0:05.10 73.1% 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 13:53:27 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4406 !!! WARNING: HIT 442 has a net charge of 0.5140 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: 1.508368 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): -3.495000 67.31000 ymin,ymax (A): -12.61800 38.32500 zmin,zma (A): -19.70400 45.31700 x,y,z range (A): 70.80500 50.94300 65.02100 scale (grids/A): 1.508368 object centre (A): 31.90750 12.85350 12.80650 number of atom coordinates read : 4406 total number of charged atoms : 4251 net assigned charge : -5.485952 assigned positive charge : 667.0689 centred at (gu) : 84.30233 89.74683 92.36884 assigned negative charge : -672.5572 centred at (gu) : 84.46604 90.06790 92.42699 start vw surface at 0.1300000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 78913 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33675 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23257 mr = 56652 m= 1925 mr = 16052 m= 29 mr = 854 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 575 time to turn everything in is 0.4000000 number of dielectric boundary points 30566 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 501 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 31852 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) : 0.5027894 object centre at (A) : 31.90750 12.85350 12.80650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0904011E-03 -7.8560347E-03 midg,1,midg; midg,igrid,midg 2.2847587E-03 -9.7615793E-03 1,midg,midg; igrid,midg,midg 7.0306300E-03 -4.7244513E-03 gauss-seidel spectral radius is 0.9979865 estimated iterations to convergence 177 setup time was (sec) 0.6200000 now iterating at: 13:53:28 rms-change max change #iterations 3.497279 168.7986 at 10iterations 1.390579 55.92183 at 20iterations 0.5531784 18.58048 at 30iterations 0.2217795 7.792267 at 40iterations 8.8350914E-02 3.131207 at 50iterations 3.5402868E-02 1.196482 at 60iterations 1.4297172E-02 0.4831161 at 70iterations 5.8137053E-03 0.1956987 at 80iterations 2.4556352E-03 8.5391998E-02 at 90iterations 1.1016014E-03 3.6689758E-02 at 100iterations 5.4934062E-04 2.1160126E-02 at 110iterations 3.0646700E-04 1.0990143E-02 at 120iterations finished qdiffx linear iterations at : 13:53:35 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 3.0646700E-04 1.0990143E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 13:53:36 7.836u 0.198s 0:09.25 86.7% 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 Mon Oct 10 2011 at 13:54:00 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4406 !!! WARNING: HIT 442 has a net charge of 0.5140 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: 2.262552 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): -3.495000 67.31000 ymin,ymax (A): -12.61800 38.32500 zmin,zma (A): -19.70400 45.31700 x,y,z range (A): 70.80500 50.94300 65.02100 scale (grids/A): 2.262552 object centre (A): 31.90750 12.85350 12.80650 number of atom coordinates read : 4406 total number of charged atoms : 4251 net assigned charge : -5.485952 assigned positive charge : 667.0689 centred at (gu) : 81.45304 89.62010 93.55310 assigned negative charge : -672.5572 centred at (gu) : 81.69904 90.10162 93.64041 start vw surface at 0.1200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 184508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33675 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 84368 mr = 138773 m= 21030 mr = 67614 m= 2777 mr = 15569 m= 108 mr = 1733 m= 4 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 2132 time to turn everything in is 0.9500000 number of dielectric boundary points 69082 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 33890 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) : 1.508368 object centre at (A) : 31.90750 12.85350 12.80650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2430961 -0.1843084 midg,1,midg; midg,igrid,midg 2.4920180E-02 -0.1567062 1,midg,midg; igrid,midg,midg 0.1857537 -0.3893972 gauss-seidel spectral radius is 0.9990988 estimated iterations to convergence 263 setup time was (sec) 1.180000 now iterating at: 13:54:01 rms-change max change #iterations 9.529907 243.1078 at 10iterations 5.322841 175.4007 at 20iterations 2.952519 69.07430 at 30iterations 1.627142 33.52020 at 40iterations 0.8928168 20.31076 at 50iterations 0.4892644 9.712574 at 60iterations 0.2675849 5.441978 at 70iterations 0.1460820 3.045837 at 80iterations 7.9643227E-02 1.792160 at 90iterations 4.3382566E-02 0.9476147 at 100iterations 2.3624724E-02 0.4719164 at 110iterations 1.2870035E-02 0.2530518 at 120iterations 7.0355241E-03 0.1455927 at 130iterations 3.8586769E-03 9.5451355E-02 at 140iterations 2.1326975E-03 4.4218063E-02 at 150iterations 1.2003931E-03 2.3685455E-02 at 160iterations 6.9241377E-04 1.4251709E-02 at 170iterations 4.1663702E-04 9.1972351E-03 at 180iterations finished qdiffx linear iterations at : 13:54:12 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 4.1663702E-04 9.1972351E-03 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.61000 DelPhi exited at 13:54:13 12.612u 0.208s 0:13.12 97.6% 0+0k 0+0io 0pf+0w