Tue Oct 11 03:59:35 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 03:59:35 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 !!! WARNING: ARG 217 has a net charge of 1.2720 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6353512 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): -11.62600 36.90700 ymin,ymax (A): -25.80700 22.47300 zmin,zma (A): -10.61400 45.41800 x,y,z range (A): 48.53300 48.28000 56.03201 scale (grids/A): 0.6353512 object centre (A): 12.64050 -1.667000 17.40200 number of atom coordinates read : 2726 total number of charged atoms : 2574 net assigned charge : 1.412010 assigned positive charge : 409.7188 centred at (gu) : 90.22381 90.24047 91.93670 assigned negative charge : -408.3074 centred at (gu) : 89.98586 90.08722 91.87230 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7231 nv = 96 ne = 84 npr = 56060 no. pairs analyzed = 56060 no. exposed pairs = 3274 no. arc points = 22908 no. surface atoms = 1099 nbur = 1627 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 412 mr = 4080 m= 0 mr = 49 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2298 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8846 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5195766E-09 1.2954964E-08 midg,1,midg; midg,igrid,midg -1.4410083E-08 1.8762851E-08 1,midg,midg; igrid,midg,midg -2.3524274E-08 2.7868591E-08 gauss-seidel spectral radius is 0.9871734 estimated iterations to convergence 72 setup time was (sec) 0.6200000 now iterating at: 03:59:36 rms-change max change #iterations 0.1447203 26.13741 at 10iterations 1.4360011E-02 2.022558 at 20iterations 1.4517508E-03 0.2162666 at 30iterations 1.5414809E-04 2.0965576E-02 at 40iterations 2.0458805E-05 3.2196045E-03 at 50iterations finished qdiffx linear iterations at : 03:59:39 total time elapsed so far: 3.800000 # loops : 50 mean,max change (kT/e) : 2.0458805E-05 3.2196045E-03 energy calculations done at 3.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.980000 DelPhi exited at 03:59:40 3.980u 0.243s 0:04.70 89.7% 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 03:59:40 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 !!! WARNING: ARG 217 has a net charge of 1.2720 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.906054 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): -11.62600 36.90700 ymin,ymax (A): -25.80700 22.47300 zmin,zma (A): -10.61400 45.41800 x,y,z range (A): 48.53300 48.28000 56.03201 scale (grids/A): 1.906054 object centre (A): 12.64050 -1.667000 17.40200 number of atom coordinates read : 2726 total number of charged atoms : 2574 net assigned charge : 1.412010 assigned positive charge : 409.7188 centred at (gu) : 90.67095 90.72062 95.80933 assigned negative charge : -408.3074 centred at (gu) : 89.95705 90.26107 95.61665 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 78551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22908 grid for indexing accessible points = 1.400000 m= 28409 mr = 55403 m= 4356 mr = 21090 m= 241 mr = 2713 m= 0 mr = 80 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 576 time to turn everything in is 0.6700000 number of dielectric boundary points 32271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 20268 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) : 0.6353512 object centre at (A) : 12.64050 -1.667000 17.40200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8469679E-02 -1.3920464E-02 midg,1,midg; midg,igrid,midg -8.6084604E-03 2.8193468E-02 1,midg,midg; igrid,midg,midg -7.1268850E-03 5.2720692E-02 gauss-seidel spectral radius is 0.9986483 estimated iterations to convergence 216 setup time was (sec) 0.9600000 now iterating at: 03:59:41 rms-change max change #iterations 4.353477 173.8373 at 10iterations 2.044855 69.81823 at 20iterations 0.9628381 38.43379 at 30iterations 0.4544356 14.30843 at 40iterations 0.2144789 7.028834 at 50iterations 0.1008463 3.665092 at 60iterations 4.7422685E-02 1.515045 at 70iterations 2.2397291E-02 0.7109938 at 80iterations 1.0521329E-02 0.3147011 at 90iterations 4.9553071E-03 0.1489072 at 100iterations 2.3405396E-03 7.1754456E-02 at 110iterations 1.1014339E-03 3.4097672E-02 at 120iterations finished qdiffx linear iterations at : 03:59:49 total time elapsed so far: 9.020000 # loops : 120 mean,max change (kT/e) : 1.1014339E-03 3.4097672E-02 energy calculations done at 9.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.170000 DelPhi exited at 03:59:50 9.175u 0.308s 0:10.27 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 Tue Oct 11 2011 at 03:59:50 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 !!! WARNING: ARG 217 has a net charge of 1.2720 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.859080 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): -11.62600 36.90700 ymin,ymax (A): -25.80700 22.47300 zmin,zma (A): -10.61400 45.41800 x,y,z range (A): 48.53300 48.28000 56.03201 scale (grids/A): 2.859080 object centre (A): 12.64050 -1.667000 17.40200 number of atom coordinates read : 2726 total number of charged atoms : 2574 net assigned charge : 1.412010 assigned positive charge : 409.7188 centred at (gu) : 91.00625 91.08076 98.71394 assigned negative charge : -408.3074 centred at (gu) : 89.93557 90.39170 98.42490 start vw surface at 0.1700000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 181540 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22908 grid for indexing accessible points = 1.400000 m= 92447 mr = 133694 m= 32879 mr = 76087 m= 7680 mr = 26487 m= 1060 mr = 5808 m= 57 mr = 688 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 1825 time to turn everything in is 1.740000 number of dielectric boundary points 72868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 20583 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) : 1.906054 object centre at (A) : 12.64050 -1.667000 17.40200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.002252 4.8284411E-02 midg,1,midg; midg,igrid,midg -0.1064088 0.3375794 1,midg,midg; igrid,midg,midg -8.4138932E-03 0.4862390 gauss-seidel spectral radius is 0.9992576 estimated iterations to convergence 290 setup time was (sec) 2.050000 now iterating at: 03:59:52 rms-change max change #iterations 10.15857 449.0695 at 10iterations 5.933095 143.3032 at 20iterations 3.456381 74.67979 at 30iterations 2.003489 49.08089 at 40iterations 1.160659 24.55634 at 50iterations 0.6707415 12.53652 at 60iterations 0.3875875 7.230728 at 70iterations 0.2236618 4.342285 at 80iterations 0.1289405 2.457785 at 90iterations 7.4399687E-02 1.216874 at 100iterations 4.2898528E-02 0.8452454 at 110iterations 2.4677085E-02 0.4444065 at 120iterations 1.4214234E-02 0.2792015 at 130iterations 8.2013104E-03 0.1512680 at 140iterations 4.7490764E-03 7.9761505E-02 at 150iterations 2.7510975E-03 5.2904129E-02 at 160iterations 1.6042520E-03 2.7379513E-02 at 170iterations 9.4471674E-04 1.6792297E-02 at 180iterations finished qdiffx linear iterations at : 04:00:06 total time elapsed so far: 15.32000 # loops : 180 mean,max change (kT/e) : 9.4471674E-04 1.6792297E-02 energy calculations done at 15.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.49000 DelPhi exited at 04:00:07 15.496u 0.287s 0:16.53 95.4% 0+0k 0+0io 0pf+0w