Mon Oct 10 13:55:31 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 13:55:31 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 = 2359 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: 0.6991358 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): -0.3620000 45.67000 ymin,ymax (A): 35.28100 86.20100 zmin,zma (A): -23.63900 25.02500 x,y,z range (A): 46.03200 50.92001 48.66400 scale (grids/A): 0.6991358 object centre (A): 22.65400 60.74100 0.6929998 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500017 assigned positive charge : 357.8471 centred at (gu) : 89.74948 90.02745 91.41547 assigned negative charge : -356.3476 centred at (gu) : 89.83916 90.22023 91.34700 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7845 nv = 96 ne = 84 npr = 47771 no. pairs analyzed = 47771 no. exposed pairs = 2965 no. arc points = 20575 no. surface atoms = 1000 nbur = 1359 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 493 mr = 4397 m= 6 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3864 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1999 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8840 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6702412E-08 5.5365398E-08 midg,1,midg; midg,igrid,midg 9.7744092E-08 -8.2477690E-08 1,midg,midg; igrid,midg,midg 5.4075432E-08 -3.0796539E-08 gauss-seidel spectral radius is 0.9893678 estimated iterations to convergence 79 setup time was (sec) 0.5500000 now iterating at: 13:55:32 rms-change max change #iterations 0.2043893 29.59699 at 10iterations 2.4591403E-02 3.421997 at 20iterations 3.4341423E-03 0.4578247 at 30iterations 6.8634527E-04 9.8329544E-02 at 40iterations 2.0344787E-04 3.0029297E-02 at 50iterations finished qdiffx linear iterations at : 13:55:34 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 2.0344787E-04 3.0029297E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 13:55:35 3.326u 0.180s 0:04.10 85.3% 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 13:55:35 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 = 2359 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: 2.097407 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): -0.3620000 45.67000 ymin,ymax (A): 35.28100 86.20100 zmin,zma (A): -23.63900 25.02500 x,y,z range (A): 46.03200 50.92001 48.66400 scale (grids/A): 2.097407 object centre (A): 22.65400 60.74100 0.6929998 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500017 assigned positive charge : 357.8471 centred at (gu) : 89.24793 90.08183 94.24591 assigned negative charge : -356.3476 centred at (gu) : 89.51736 90.66050 94.04089 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 83298 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20575 grid for indexing accessible points = 1.400000 m= 31952 mr = 58205 m= 5653 mr = 23919 m= 465 mr = 3665 m= 5 mr = 218 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 35366 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17587 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) : 0.6991358 object centre at (A) : 22.65400 60.74100 0.6929998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0983241E-03 1.7775271E-02 midg,1,midg; midg,igrid,midg 9.8635010E-02 -6.2111676E-02 1,midg,midg; igrid,midg,midg 3.4240121E-03 -8.4696133E-03 gauss-seidel spectral radius is 0.9988416 estimated iterations to convergence 233 setup time was (sec) 0.9300000 now iterating at: 13:55:36 rms-change max change #iterations 4.896308 232.1139 at 10iterations 2.422377 74.61393 at 20iterations 1.205422 40.08003 at 30iterations 0.5987145 16.66785 at 40iterations 0.2983355 9.100996 at 50iterations 0.1484670 4.355867 at 60iterations 7.3982544E-02 2.495018 at 70iterations 3.6956437E-02 1.011122 at 80iterations 1.8534144E-02 0.5251999 at 90iterations 9.3792956E-03 0.2762041 at 100iterations 4.7695860E-03 0.1314421 at 110iterations 2.5062133E-03 7.8800201E-02 at 120iterations finished qdiffx linear iterations at : 13:55:43 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 2.5062133E-03 7.8800201E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 13:55:44 7.625u 0.204s 0:08.48 92.2% 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 13:55:44 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 = 2359 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: 3.146111 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): -0.3620000 45.67000 ymin,ymax (A): 35.28100 86.20100 zmin,zma (A): -23.63900 25.02500 x,y,z range (A): 46.03200 50.92001 48.66400 scale (grids/A): 3.146111 object centre (A): 22.65400 60.74100 0.6929998 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500017 assigned positive charge : 357.8471 centred at (gu) : 88.87185 90.12261 96.36877 assigned negative charge : -356.3476 centred at (gu) : 89.27596 90.99067 96.06121 start vw surface at 0.1300000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 191854 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20575 grid for indexing accessible points = 1.400000 m= 101349 mr = 140348 m= 39446 mr = 83607 m= 10518 mr = 32106 m= 1872 mr = 8028 m= 176 mr = 1337 m= 8 mr = 103 m= 0 mr = 3 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.850000 number of dielectric boundary points 79691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 17736 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) : 2.097407 object centre at (A) : 22.65400 60.74100 0.6929998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2083769 0.4101351 midg,1,midg; midg,igrid,midg 1.616938 -0.7040475 1,midg,midg; igrid,midg,midg -1.5380816E-02 -2.8869852E-02 gauss-seidel spectral radius is 0.9993036 estimated iterations to convergence 299 setup time was (sec) 2.150000 now iterating at: 13:55:46 rms-change max change #iterations 10.93300 367.6486 at 10iterations 6.495141 152.5724 at 20iterations 3.840493 83.71507 at 30iterations 2.270430 40.67586 at 40iterations 1.342611 23.70748 at 50iterations 0.7915002 13.44913 at 60iterations 0.4665349 8.494083 at 70iterations 0.2742655 5.184416 at 80iterations 0.1608470 2.795725 at 90iterations 9.4567761E-02 1.590958 at 100iterations 5.5654529E-02 0.9055710 at 110iterations 3.2859694E-02 0.5413895 at 120iterations 1.9485909E-02 0.3419056 at 130iterations 1.1684671E-02 0.1922302 at 140iterations 7.1719978E-03 0.1364937 at 150iterations 4.5564757E-03 9.0858459E-02 at 160iterations 3.0508824E-03 6.8161011E-02 at 170iterations 2.1760138E-03 4.5875549E-02 at 180iterations finished qdiffx linear iterations at : 13:55:57 total time elapsed so far: 13.01000 # loops : 180 mean,max change (kT/e) : 2.1760138E-03 4.5875549E-02 energy calculations done at 13.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 13:55:57 13.173u 0.228s 0:13.82 96.8% 0+0k 0+0io 0pf+0w