Sat Oct 8 14:50:43 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 Sat Oct 8 2011 at 14:50:43 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2968 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6368629 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): -12.15000 43.27000 ymin,ymax (A): -24.01400 22.33200 zmin,zma (A): -7.797000 48.10200 x,y,z range (A): 55.42000 46.34600 55.89900 scale (grids/A): 0.6368629 object centre (A): 15.56000 -0.8410006 20.15250 number of atom coordinates read : 2968 total number of charged atoms : 2823 net assigned charge : 1.242007 assigned positive charge : 445.4957 centred at (gu) : 88.79374 90.03919 91.49621 assigned negative charge : -444.2544 centred at (gu) : 88.72037 89.89027 91.48846 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8001 nv = 96 ne = 84 npr = 62061 no. pairs analyzed = 62061 no. exposed pairs = 3365 no. arc points = 23723 no. surface atoms = 1149 nbur = 1819 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 411 mr = 4659 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2340 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9739 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0901839E-10 3.7273717E-09 midg,1,midg; midg,igrid,midg -1.6571487E-08 1.9812182E-08 1,midg,midg; igrid,midg,midg -9.5179535E-09 8.2053182E-09 gauss-seidel spectral radius is 0.9872555 estimated iterations to convergence 72 setup time was (sec) 0.6500000 now iterating at: 14:50:44 rms-change max change #iterations 0.1528195 19.76758 at 10iterations 1.5291314E-02 2.275089 at 20iterations 1.5915378E-03 0.2113132 at 30iterations 1.8017336E-04 2.4297714E-02 at 40iterations 2.6787322E-05 4.1828156E-03 at 50iterations finished qdiffx linear iterations at : 14:50:47 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 2.6787322E-05 4.1828156E-03 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 14:50:47 4.128u 0.273s 0:04.70 93.4% 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 Sat Oct 8 2011 at 14:50:47 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2968 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.910589 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): -12.15000 43.27000 ymin,ymax (A): -24.01400 22.33200 zmin,zma (A): -7.797000 48.10200 x,y,z range (A): 55.42000 46.34600 55.89900 scale (grids/A): 1.910589 object centre (A): 15.56000 -0.8410006 20.15250 number of atom coordinates read : 2968 total number of charged atoms : 2823 net assigned charge : 1.242007 assigned positive charge : 445.4957 centred at (gu) : 86.38073 90.11729 94.48777 assigned negative charge : -444.2544 centred at (gu) : 86.16101 89.67065 94.46485 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 87280 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23723 grid for indexing accessible points = 1.400000 m= 31268 mr = 62879 m= 4496 mr = 23349 m= 282 mr = 2733 m= 1 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 34262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 22189 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) : 0.6368629 object centre at (A) : 15.56000 -0.8410006 20.15250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0116224E-03 9.0196114E-03 midg,1,midg; midg,igrid,midg -6.3915667E-04 2.8015276E-02 1,midg,midg; igrid,midg,midg -3.6326446E-02 2.4139604E-02 gauss-seidel spectral radius is 0.9986730 estimated iterations to convergence 217 setup time was (sec) 1.070000 now iterating at: 14:50:49 rms-change max change #iterations 4.652453 222.6965 at 10iterations 2.206745 69.64253 at 20iterations 1.049408 32.84416 at 30iterations 0.4964874 14.56215 at 40iterations 0.2353336 6.659568 at 50iterations 0.1115986 3.401005 at 60iterations 5.2753847E-02 1.443398 at 70iterations 2.4985718E-02 0.7394862 at 80iterations 1.1869617E-02 0.3565741 at 90iterations 5.6445282E-03 0.1666336 at 100iterations 2.6784544E-03 8.0502510E-02 at 110iterations 1.2763503E-03 3.8818359E-02 at 120iterations finished qdiffx linear iterations at : 14:50:57 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 1.2763503E-03 3.8818359E-02 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 14:50:58 9.652u 0.298s 0:10.25 96.9% 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 Sat Oct 8 2011 at 14:50:58 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2968 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.865883 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): -12.15000 43.27000 ymin,ymax (A): -24.01400 22.33200 zmin,zma (A): -7.797000 48.10200 x,y,z range (A): 55.42000 46.34600 55.89900 scale (grids/A): 2.865883 object centre (A): 15.56000 -0.8410006 20.15250 number of atom coordinates read : 2968 total number of charged atoms : 2823 net assigned charge : 1.242007 assigned positive charge : 445.4957 centred at (gu) : 84.57095 90.17577 96.73132 assigned negative charge : -444.2544 centred at (gu) : 84.24147 89.50585 96.69724 start vw surface at 0.1700000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 201921 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23723 grid for indexing accessible points = 1.400000 m= 102593 mr = 151499 m= 35552 mr = 85290 m= 8073 mr = 28555 m= 1204 mr = 6010 m= 74 mr = 820 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.950000 number of dielectric boundary points 77219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 22584 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) : 1.910589 object centre at (A) : 15.56000 -0.8410006 20.15250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1470005E-02 0.2254597 midg,1,midg; midg,igrid,midg 9.6920773E-04 0.2972729 1,midg,midg; igrid,midg,midg -0.2760566 0.3312037 gauss-seidel spectral radius is 0.9992731 estimated iterations to convergence 293 setup time was (sec) 2.280000 now iterating at: 14:51:00 rms-change max change #iterations 10.74611 480.1407 at 10iterations 6.282269 122.1589 at 20iterations 3.644396 71.91235 at 30iterations 2.116600 47.52102 at 40iterations 1.224577 22.55672 at 50iterations 0.7097619 12.91484 at 60iterations 0.4110254 7.110688 at 70iterations 0.2380331 3.961548 at 80iterations 0.1376337 2.261229 at 90iterations 7.9422198E-02 1.382894 at 100iterations 4.5823224E-02 0.8103828 at 110iterations 2.6522787E-02 0.4954605 at 120iterations 1.5328664E-02 0.2682328 at 130iterations 8.8499971E-03 0.1491203 at 140iterations 5.1224944E-03 8.5937500E-02 at 150iterations 2.9656466E-03 4.8065901E-02 at 160iterations 1.7256194E-03 2.8464317E-02 at 170iterations 1.0033356E-03 1.6990662E-02 at 180iterations finished qdiffx linear iterations at : 14:51:14 total time elapsed so far: 16.21000 # loops : 180 mean,max change (kT/e) : 1.0033356E-03 1.6990662E-02 energy calculations done at 16.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.39000 DelPhi exited at 14:51:15 16.396u 0.320s 0:17.02 98.1% 0+0k 0+0io 0pf+0w