Tue Nov 22 14:12:37 PST 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 Tue Nov 22 2011 at 14:12:42 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 0.6433657 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): -4.024000 35.07900 ymin,ymax (A): -4.657000 48.54400 zmin,zma (A): -24.05300 31.28100 x,y,z range (A): 39.10300 53.20100 55.33400 scale (grids/A): 0.6433657 object centre (A): 15.52750 21.94350 3.614000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 290.6260 centred at (gu) : 90.21623 92.98210 90.03257 assigned negative charge : -285.6263 centred at (gu) : 90.25620 93.05873 89.98195 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5613 nv = 96 ne = 84 npr = 40250 no. pairs analyzed = 40250 no. exposed pairs = 2371 no. arc points = 17063 no. surface atoms = 803 nbur = 1159 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 295 mr = 3172 m= 0 mr = 43 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2200000 number of dielectric boundary points 2693 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1678 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6489 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4296650E-09 1.2959099E-08 midg,1,midg; midg,igrid,midg 8.2235712E-09 1.3743066E-09 1,midg,midg; igrid,midg,midg 1.1363568E-08 4.6454165E-09 gauss-seidel spectral radius is 0.9874267 estimated iterations to convergence 73 setup time was (sec) 0.4600000 now iterating at: 14:12:45 rms-change max change #iterations 0.1279652 19.30317 at 10iterations 1.2822907E-02 2.338463 at 20iterations 1.2925614E-03 0.2070045 at 30iterations 1.2933314E-04 2.2315979E-02 at 40iterations 1.2843081E-05 1.8997192E-03 at 50iterations finished qdiffx linear iterations at : 14:12:53 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 1.2843081E-05 1.8997192E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 14:12:56 3.150u 0.195s 0:15.40 21.6% 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 Tue Nov 22 2011 at 14:13:01 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 1.930097 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): -4.024000 35.07900 ymin,ymax (A): -4.657000 48.54400 zmin,zma (A): -24.05300 31.28100 x,y,z range (A): 39.10300 53.20100 55.33400 scale (grids/A): 1.930097 object centre (A): 15.52750 21.94350 3.614000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 290.6260 centred at (gu) : 90.64857 98.94614 90.09774 assigned negative charge : -285.6263 centred at (gu) : 90.76865 99.17635 89.94591 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 59767 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17063 grid for indexing accessible points = 1.400000 m= 22831 mr = 41515 m= 3542 mr = 17674 m= 172 mr = 2345 m= 1 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 2019 time to turn everything in is 0.4200000 number of dielectric boundary points 24697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 14422 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) : 0.6433657 object centre at (A) : 15.52750 21.94350 3.614000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9374636E-02 2.4377031E-02 midg,1,midg; midg,igrid,midg 3.4028817E-02 9.5282989E-03 1,midg,midg; igrid,midg,midg 4.4157673E-03 -2.1117620E-04 gauss-seidel spectral radius is 0.9985912 estimated iterations to convergence 211 setup time was (sec) 0.7000000 now iterating at: 14:13:07 rms-change max change #iterations 3.661218 200.2666 at 10iterations 1.693982 59.83276 at 20iterations 0.7873679 29.18614 at 30iterations 0.3646568 12.47042 at 40iterations 0.1679246 5.818220 at 50iterations 7.7552542E-02 2.682596 at 60iterations 3.5894006E-02 1.181255 at 70iterations 1.6628036E-02 0.5451813 at 80iterations 7.6587447E-03 0.2490330 at 90iterations 3.5611321E-03 0.1373901 at 100iterations 1.6450800E-03 5.7695389E-02 at 110iterations 7.6257408E-04 2.6789665E-02 at 120iterations finished qdiffx linear iterations at : 14:13:26 total time elapsed so far: 7.080000 # loops : 120 mean,max change (kT/e) : 7.6257408E-04 2.6789665E-02 energy calculations done at 7.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.250000 DelPhi exited at 14:13:31 7.256u 0.164s 0:30.23 24.5% 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 Tue Nov 22 2011 at 14:13:33 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 2.895146 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): -4.024000 35.07900 ymin,ymax (A): -4.657000 48.54400 zmin,zma (A): -24.05300 31.28100 x,y,z range (A): 39.10300 53.20100 55.33400 scale (grids/A): 2.895146 object centre (A): 15.52750 21.94350 3.614000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 290.6260 centred at (gu) : 90.97276 103.4192 90.14668 assigned negative charge : -285.6263 centred at (gu) : 91.15321 103.7645 89.91887 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 138236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17063 grid for indexing accessible points = 1.400000 m= 72311 mr = 100389 m= 27773 mr = 60472 m= 6296 mr = 23407 m= 776 mr = 4971 m= 50 mr = 548 m= 0 mr = 24 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 6732 time to turn everything in is 1.030000 number of dielectric boundary points 55631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 14640 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) : 1.930097 object centre at (A) : 15.52750 21.94350 3.614000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.111977 8.0688849E-02 midg,1,midg; midg,igrid,midg 0.3352386 -4.7035650E-03 1,midg,midg; igrid,midg,midg 2.8071685E-02 -8.5282192E-04 gauss-seidel spectral radius is 0.9992340 estimated iterations to convergence 285 setup time was (sec) 1.300000 now iterating at: 14:13:41 rms-change max change #iterations 8.537254 366.8237 at 10iterations 4.900463 136.9871 at 20iterations 2.786478 66.34489 at 30iterations 1.578861 32.27654 at 40iterations 0.9011173 18.75610 at 50iterations 0.5117428 10.54618 at 60iterations 0.2898432 6.020144 at 70iterations 0.1647663 3.130587 at 80iterations 9.3375832E-02 1.793233 at 90iterations 5.3069852E-02 1.045503 at 100iterations 3.0137928E-02 0.6062851 at 110iterations 1.7043959E-02 0.3165169 at 120iterations 9.6809892E-03 0.1933002 at 130iterations 5.4883864E-03 0.1023483 at 140iterations 3.1243947E-03 6.3827515E-02 at 150iterations 1.7734007E-03 3.4803391E-02 at 160iterations 1.0053238E-03 2.3164749E-02 at 170iterations 5.7221355E-04 1.0960340E-02 at 180iterations finished qdiffx linear iterations at : 14:14:10 total time elapsed so far: 10.89000 # loops : 180 mean,max change (kT/e) : 5.7221355E-04 1.0960340E-02 energy calculations done at 10.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.07000 DelPhi exited at 14:14:13 11.068u 0.184s 0:41.51 27.0% 0+0k 0+0io 0pf+0w