Tue Oct 11 06:36:17 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 Tue Oct 11 2011 at 06:36:17 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 = 2056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7077253 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): -20.18400 24.61000 ymin,ymax (A): -28.62100 12.09900 zmin,zma (A): -13.50500 36.79700 x,y,z range (A): 44.79400 40.72000 50.30200 scale (grids/A): 0.7077253 object centre (A): 2.213000 -8.261000 11.64600 number of atom coordinates read : 2056 total number of charged atoms : 1928 net assigned charge : 7.500009 assigned positive charge : 311.7690 centred at (gu) : 89.84859 90.25716 89.36074 assigned negative charge : -304.2692 centred at (gu) : 89.67232 90.23450 89.32460 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6933 nv = 96 ne = 84 npr = 41388 no. pairs analyzed = 41388 no. exposed pairs = 2490 no. arc points = 16864 no. surface atoms = 842 nbur = 1214 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 3995 m= 2 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1590 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7721 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2218017E-08 7.2192421E-08 midg,1,midg; midg,igrid,midg 5.0543363E-08 7.8743085E-08 1,midg,midg; igrid,midg,midg -2.3869951E-08 1.4378413E-07 gauss-seidel spectral radius is 0.9895894 estimated iterations to convergence 80 setup time was (sec) 0.3600000 now iterating at: 06:36:18 rms-change max change #iterations 0.1952293 32.53669 at 10iterations 2.4398783E-02 3.560341 at 20iterations 3.1306653E-03 0.4448308 at 30iterations 4.5580679E-04 6.2908173E-02 at 40iterations 9.6067219E-05 1.3229370E-02 at 50iterations finished qdiffx linear iterations at : 06:36:21 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 9.6067219E-05 1.3229370E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 06:36:21 3.346u 0.165s 0:03.89 89.9% 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 Oct 11 2011 at 06:36:21 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 = 2056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.123176 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): -20.18400 24.61000 ymin,ymax (A): -28.62100 12.09900 zmin,zma (A): -13.50500 36.79700 x,y,z range (A): 44.79400 40.72000 50.30200 scale (grids/A): 2.123176 object centre (A): 2.213000 -8.261000 11.64600 number of atom coordinates read : 2056 total number of charged atoms : 1928 net assigned charge : 7.500009 assigned positive charge : 311.7690 centred at (gu) : 89.54575 90.77155 88.08234 assigned negative charge : -304.2692 centred at (gu) : 89.01711 90.70355 87.97391 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73979 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16864 grid for indexing accessible points = 1.400000 m= 29402 mr = 52708 m= 5647 mr = 22223 m= 483 mr = 3735 m= 18 mr = 251 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 30609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15322 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) : 0.7077253 object centre at (A) : 2.213000 -8.261000 11.64600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7527011E-02 4.5961905E-02 midg,1,midg; midg,igrid,midg 4.5369146E-03 3.1452294E-02 1,midg,midg; igrid,midg,midg 1.6206568E-02 4.0478960E-02 gauss-seidel spectral radius is 0.9988287 estimated iterations to convergence 231 setup time was (sec) 0.5700000 now iterating at: 06:36:22 rms-change max change #iterations 4.550613 188.1541 at 10iterations 2.248639 77.60926 at 20iterations 1.114508 35.61974 at 30iterations 0.5523932 16.79225 at 40iterations 0.2751036 8.484394 at 50iterations 0.1364593 4.215341 at 60iterations 6.7732371E-02 2.129887 at 70iterations 3.3538405E-02 0.9973202 at 80iterations 1.6690310E-02 0.4860306 at 90iterations 8.3342334E-03 0.2635221 at 100iterations 4.1558477E-03 0.1321106 at 110iterations 2.0947533E-03 6.5193176E-02 at 120iterations finished qdiffx linear iterations at : 06:36:29 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 2.0947533E-03 6.5193176E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 06:36:30 7.797u 0.209s 0:08.59 93.0% 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 Oct 11 2011 at 06:36:30 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 = 2056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.184764 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): -20.18400 24.61000 ymin,ymax (A): -28.62100 12.09900 zmin,zma (A): -13.50500 36.79700 x,y,z range (A): 44.79400 40.72000 50.30200 scale (grids/A): 3.184764 object centre (A): 2.213000 -8.261000 11.64600 number of atom coordinates read : 2056 total number of charged atoms : 1928 net assigned charge : 7.500009 assigned positive charge : 311.7690 centred at (gu) : 89.31859 91.15722 87.12356 assigned negative charge : -304.2692 centred at (gu) : 88.52561 91.05542 86.96089 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 170811 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16864 grid for indexing accessible points = 1.400000 m= 91875 mr = 127033 m= 37112 mr = 76396 m= 10624 mr = 30472 m= 2068 mr = 8241 m= 240 mr = 1465 m= 4 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.130000 number of dielectric boundary points 68972 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 15424 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) : 2.123176 object centre at (A) : 2.213000 -8.261000 11.64600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7131740 0.3744382 midg,1,midg; midg,igrid,midg 1.7316785E-02 0.2382012 1,midg,midg; igrid,midg,midg 0.2676405 0.3005702 gauss-seidel spectral radius is 0.9992921 estimated iterations to convergence 297 setup time was (sec) 1.350000 now iterating at: 06:36:31 rms-change max change #iterations 10.11539 311.5141 at 10iterations 5.966225 191.6255 at 20iterations 3.523007 77.35533 at 30iterations 2.074018 37.51214 at 40iterations 1.217949 24.59814 at 50iterations 0.7153803 13.28600 at 60iterations 0.4189906 8.197765 at 70iterations 0.2452324 4.000651 at 80iterations 0.1436343 2.872328 at 90iterations 8.4138878E-02 1.780523 at 100iterations 4.9140293E-02 0.9112701 at 110iterations 2.8910825E-02 0.4991951 at 120iterations 1.7010119E-02 0.2861099 at 130iterations 1.0099436E-02 0.1803627 at 140iterations 6.0842675E-03 0.1077509 at 150iterations 3.7430630E-03 7.5916290E-02 at 160iterations 2.4004132E-03 4.4277191E-02 at 170iterations 1.6182038E-03 3.1646729E-02 at 180iterations finished qdiffx linear iterations at : 06:36:43 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 1.6182038E-03 3.1646729E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.68000 DelPhi exited at 06:36:43 12.687u 0.232s 0:13.24 97.5% 0+0k 0+0io 0pf+0w