Tue Oct 11 06:43:13 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 06:43:13 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2199 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7076972 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): 2.386000 47.58000 ymin,ymax (A): 0.6220001 40.52400 zmin,zma (A): -3.356000 46.94800 x,y,z range (A): 45.19400 39.90200 50.30400 scale (grids/A): 0.7076972 object centre (A): 24.98300 20.57300 21.79600 number of atom coordinates read : 2199 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 90.05671 90.57449 90.46677 assigned negative charge : -303.7472 centred at (gu) : 90.23898 90.55708 90.50629 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6927 nv = 96 ne = 84 npr = 39943 no. pairs analyzed = 39943 no. exposed pairs = 2469 no. arc points = 16927 no. surface atoms = 841 nbur = 1358 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 431 mr = 3953 m= 4 mr = 71 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 0.2600000 number of dielectric boundary points 3338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1623 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7679 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5866588E-08 4.8621605E-08 midg,1,midg; midg,igrid,midg 4.9804591E-08 8.0588421E-08 1,midg,midg; igrid,midg,midg 1.4885116E-07 -2.6364404E-08 gauss-seidel spectral radius is 0.9895875 estimated iterations to convergence 80 setup time was (sec) 0.6000000 now iterating at: 06:43:14 rms-change max change #iterations 0.1978359 28.49343 at 10iterations 2.4740346E-02 3.409515 at 20iterations 3.1371117E-03 0.4270248 at 30iterations 4.6618324E-04 6.2305450E-02 at 40iterations 9.8047691E-05 1.3073921E-02 at 50iterations finished qdiffx linear iterations at : 06:43:18 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 9.8047691E-05 1.3073921E-02 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 06:43:19 4.480u 0.381s 0:05.34 91.0% 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 06:43:19 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2199 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.123091 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): 2.386000 47.58000 ymin,ymax (A): 0.6220001 40.52400 zmin,zma (A): -3.356000 46.94800 x,y,z range (A): 45.19400 39.90200 50.30400 scale (grids/A): 2.123091 object centre (A): 24.98300 20.57300 21.79600 number of atom coordinates read : 2199 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 90.17034 91.72325 91.40018 assigned negative charge : -303.7472 centred at (gu) : 90.71705 91.67136 91.51904 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 74058 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16927 grid for indexing accessible points = 1.400000 m= 29346 mr = 52733 m= 5630 mr = 22244 m= 562 mr = 3784 m= 10 mr = 280 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 30565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 15188 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) : 0.7076972 object centre at (A) : 24.98300 20.57300 21.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4105191E-02 6.6512011E-02 midg,1,midg; midg,igrid,midg 5.2789366E-03 3.3713557E-02 1,midg,midg; igrid,midg,midg 4.4327699E-02 1.3127889E-02 gauss-seidel spectral radius is 0.9988281 estimated iterations to convergence 231 setup time was (sec) 0.9800000 now iterating at: 06:43:20 rms-change max change #iterations 4.571511 195.1512 at 10iterations 2.262179 74.36581 at 20iterations 1.121691 33.74750 at 30iterations 0.5562700 17.72436 at 40iterations 0.2767772 8.236419 at 50iterations 0.1370644 4.253123 at 60iterations 6.8072237E-02 2.047625 at 70iterations 3.3941049E-02 1.094198 at 80iterations 1.6902270E-02 0.5160897 at 90iterations 8.4709600E-03 0.2546635 at 100iterations 4.2349175E-03 0.1247940 at 110iterations 2.1561950E-03 6.4931393E-02 at 120iterations finished qdiffx linear iterations at : 06:43:30 total time elapsed so far: 10.45000 # loops : 120 mean,max change (kT/e) : 2.1561950E-03 6.4931393E-02 energy calculations done at 10.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.61000 DelPhi exited at 06:43:30 10.618u 0.430s 0:11.33 97.4% 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 06:43:30 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2199 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.184637 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): 2.386000 47.58000 ymin,ymax (A): 0.6220001 40.52400 zmin,zma (A): -3.356000 46.94800 x,y,z range (A): 45.19400 39.90200 50.30400 scale (grids/A): 3.184637 object centre (A): 24.98300 20.57300 21.79600 number of atom coordinates read : 2199 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 90.25547 92.58484 92.10040 assigned negative charge : -303.7472 centred at (gu) : 91.07547 92.50701 92.27853 start vw surface at 0.1000000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 170699 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16927 grid for indexing accessible points = 1.400000 m= 92173 mr = 126968 m= 36799 mr = 76659 m= 10788 mr = 30289 m= 2255 mr = 8333 m= 269 mr = 1667 m= 11 mr = 159 m= 0 mr = 5 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.900000 number of dielectric boundary points 68914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 15431 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) : 2.123091 object centre at (A) : 24.98300 20.57300 21.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3664345 0.7014584 midg,1,midg; midg,igrid,midg 7.1394397E-03 0.2575104 1,midg,midg; igrid,midg,midg 0.3378680 0.2500911 gauss-seidel spectral radius is 0.9992921 estimated iterations to convergence 297 setup time was (sec) 2.230000 now iterating at: 06:43:33 rms-change max change #iterations 10.13985 320.0402 at 10iterations 5.988750 175.8554 at 20iterations 3.531552 75.94844 at 30iterations 2.081153 43.07066 at 40iterations 1.223956 25.25975 at 50iterations 0.7189484 13.55317 at 60iterations 0.4216309 8.109432 at 70iterations 0.2472110 4.561682 at 80iterations 0.1444847 2.704884 at 90iterations 8.4624529E-02 1.446983 at 100iterations 4.9599435E-02 0.9134941 at 110iterations 2.9109856E-02 0.4915819 at 120iterations 1.7111473E-02 0.2938423 at 130iterations 1.0121820E-02 0.1876659 at 140iterations 6.0745906E-03 0.1085753 at 150iterations 3.7220859E-03 7.2975159E-02 at 160iterations 2.3647628E-03 4.6537399E-02 at 170iterations 1.5778440E-03 3.1707764E-02 at 180iterations finished qdiffx linear iterations at : 06:43:48 total time elapsed so far: 17.89000 # loops : 180 mean,max change (kT/e) : 1.5778440E-03 3.1707764E-02 energy calculations done at 17.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.06000 DelPhi exited at 06:43:49 18.067u 0.469s 0:19.07 97.1% 0+0k 0+0io 0pf+0w