Tue Oct 11 03:59:14 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 Tue Oct 11 2011 at 03:59:14 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6406219 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): -11.30400 37.28100 ymin,ymax (A): -25.76200 22.35900 zmin,zma (A): -10.38700 45.18400 x,y,z range (A): 48.58500 48.12100 55.57100 scale (grids/A): 0.6406219 object centre (A): 12.98850 -1.701500 17.39850 number of atom coordinates read : 2764 total number of charged atoms : 2611 net assigned charge : 0.1540153 assigned positive charge : 419.7128 centred at (gu) : 90.17535 90.26733 91.79870 assigned negative charge : -419.5593 centred at (gu) : 89.94009 90.14335 91.73305 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7435 nv = 96 ne = 84 npr = 57231 no. pairs analyzed = 57231 no. exposed pairs = 3352 no. arc points = 23514 no. surface atoms = 1137 nbur = 1627 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 4124 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2371 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9145 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7290301E-09 1.2392487E-08 midg,1,midg; midg,igrid,midg -1.5157205E-08 1.6586407E-08 1,midg,midg; igrid,midg,midg -2.9707296E-08 3.0473156E-08 gauss-seidel spectral radius is 0.9873849 estimated iterations to convergence 73 setup time was (sec) 0.7100000 now iterating at: 03:59:15 rms-change max change #iterations 0.1549037 21.71545 at 10iterations 1.5631864E-02 2.310104 at 20iterations 1.5935745E-03 0.1986442 at 30iterations 1.8179118E-04 2.6392937E-02 at 40iterations 2.9601621E-05 5.3730011E-03 at 50iterations finished qdiffx linear iterations at : 03:59:18 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 2.9601621E-05 5.3730011E-03 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 03:59:19 4.496u 0.393s 0:05.42 90.0% 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 03:59:19 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.921866 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): -11.30400 37.28100 ymin,ymax (A): -25.76200 22.35900 zmin,zma (A): -10.38700 45.18400 x,y,z range (A): 48.58500 48.12100 55.57100 scale (grids/A): 1.921866 object centre (A): 12.98850 -1.701500 17.39850 number of atom coordinates read : 2764 total number of charged atoms : 2611 net assigned charge : 0.1540153 assigned positive charge : 419.7128 centred at (gu) : 90.52541 90.80134 95.39552 assigned negative charge : -419.5593 centred at (gu) : 89.82030 90.42954 95.19896 start vw surface at 0.1700000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 80504 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23514 grid for indexing accessible points = 1.400000 m= 28944 mr = 56573 m= 4350 mr = 21357 m= 242 mr = 2659 m= 5 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 802 time to turn everything in is 0.8200000 number of dielectric boundary points 33381 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 20547 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) : 0.6406219 object centre at (A) : 12.98850 -1.701500 17.39850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1849768E-02 -3.8765655E-03 midg,1,midg; midg,igrid,midg -1.2160074E-02 2.4544867E-02 1,midg,midg; igrid,midg,midg -1.2543834E-02 5.6189600E-02 gauss-seidel spectral radius is 0.9986728 estimated iterations to convergence 217 setup time was (sec) 1.150000 now iterating at: 03:59:21 rms-change max change #iterations 4.510089 278.8790 at 10iterations 2.142321 77.40849 at 20iterations 1.015645 29.54850 at 30iterations 0.4824525 14.69035 at 40iterations 0.2283459 7.137140 at 50iterations 0.1082106 3.149319 at 60iterations 5.1281549E-02 1.626647 at 70iterations 2.4422027E-02 0.7809968 at 80iterations 1.1558515E-02 0.3499289 at 90iterations 5.4890448E-03 0.1604080 at 100iterations 2.6022345E-03 7.9373360E-02 at 110iterations 1.2333449E-03 3.7408829E-02 at 120iterations finished qdiffx linear iterations at : 03:59:30 total time elapsed so far: 10.48000 # loops : 120 mean,max change (kT/e) : 1.2333449E-03 3.7408829E-02 energy calculations done at 10.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.69000 DelPhi exited at 03:59:31 10.696u 0.459s 0:11.64 95.7% 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 Tue Oct 11 2011 at 03:59:31 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.882798 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): -11.30400 37.28100 ymin,ymax (A): -25.76200 22.35900 zmin,zma (A): -10.38700 45.18400 x,y,z range (A): 48.58500 48.12100 55.57100 scale (grids/A): 2.882798 object centre (A): 12.98850 -1.701500 17.39850 number of atom coordinates read : 2764 total number of charged atoms : 2611 net assigned charge : 0.1540153 assigned positive charge : 419.7128 centred at (gu) : 90.78805 91.20187 98.09308 assigned negative charge : -419.5593 centred at (gu) : 89.73028 90.64444 97.79842 start vw surface at 0.1500000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 186072 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23514 grid for indexing accessible points = 1.400000 m= 94659 mr = 136645 m= 33648 mr = 77751 m= 7852 mr = 27075 m= 1109 mr = 5842 m= 55 mr = 711 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 2885 time to turn everything in is 2.130000 number of dielectric boundary points 75349 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 20884 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) : 1.921866 object centre at (A) : 12.98850 -1.701500 17.39850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7496144 0.1819210 midg,1,midg; midg,igrid,midg -0.1423065 0.3086788 1,midg,midg; igrid,midg,midg -9.5260136E-02 0.5248639 gauss-seidel spectral radius is 0.9992671 estimated iterations to convergence 292 setup time was (sec) 2.500000 now iterating at: 03:59:34 rms-change max change #iterations 10.55489 418.6665 at 10iterations 6.199054 139.9111 at 20iterations 3.620556 71.84830 at 30iterations 2.108005 39.70853 at 40iterations 1.225525 22.17932 at 50iterations 0.7096362 13.35968 at 60iterations 0.4111902 7.451748 at 70iterations 0.2381176 4.270361 at 80iterations 0.1377178 2.405252 at 90iterations 7.9540223E-02 1.415995 at 100iterations 4.5953263E-02 0.8044815 at 110iterations 2.6590804E-02 0.4413452 at 120iterations 1.5364037E-02 0.2707844 at 130iterations 8.8967020E-03 0.1617012 at 140iterations 5.1493188E-03 9.4431877E-02 at 150iterations 2.9957544E-03 5.1691055E-02 at 160iterations 1.7417617E-03 3.7200928E-02 at 170iterations 1.0237313E-03 2.1100998E-02 at 180iterations finished qdiffx linear iterations at : 03:59:49 total time elapsed so far: 18.09000 # loops : 180 mean,max change (kT/e) : 1.0237313E-03 2.1100998E-02 energy calculations done at 18.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.31000 DelPhi exited at 03:59:50 18.311u 0.474s 0:19.39 96.8% 0+0k 0+0io 0pf+0w