Tue Oct 11 08:34:44 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 08:34:44 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 = 2783 !!! WARNING: TRP 148 has a net charge of -0.2720 !!! WARNING: ASP 292 has a net charge of -0.2720 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6568145 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): -8.365000 40.98500 ymin,ymax (A): -26.31200 21.98800 zmin,zma (A): -9.772000 44.42900 x,y,z range (A): 49.35000 48.30000 54.20100 scale (grids/A): 0.6568145 object centre (A): 16.31000 -2.162001 17.32850 number of atom coordinates read : 2783 total number of charged atoms : 2631 net assigned charge : 3.618024 assigned positive charge : 419.5555 centred at (gu) : 89.77236 90.34677 88.49516 assigned negative charge : -415.9383 centred at (gu) : 89.99796 90.15406 88.53688 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8078 nv = 96 ne = 84 npr = 56892 no. pairs analyzed = 56892 no. exposed pairs = 3356 no. arc points = 23213 no. surface atoms = 1123 nbur = 1660 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 420 mr = 4664 m= 4 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 41 time to turn everything in is 0.3700000 number of dielectric boundary points 3784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2285 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9546 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2211998E-08 6.7792591E-11 midg,1,midg; midg,igrid,midg -2.8057105E-08 4.8347097E-08 1,midg,midg; igrid,midg,midg 5.3581459E-08 -3.5176679E-08 gauss-seidel spectral radius is 0.9879988 estimated iterations to convergence 75 setup time was (sec) 0.6300000 now iterating at: 08:34:45 rms-change max change #iterations 0.1683306 21.71215 at 10iterations 1.8361649E-02 2.441109 at 20iterations 2.0314716E-03 0.2792931 at 30iterations 2.7398363E-04 3.4406185E-02 at 40iterations 5.9643658E-05 7.7857971E-03 at 50iterations finished qdiffx linear iterations at : 08:34:48 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 5.9643658E-05 7.7857971E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 08:34:49 4.160u 0.273s 0:04.75 93.2% 0+0k 0+0io 6pf+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 08:34:49 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 = 2783 !!! WARNING: TRP 148 has a net charge of -0.2720 !!! WARNING: ASP 292 has a net charge of -0.2720 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.970443 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): -8.365000 40.98500 ymin,ymax (A): -26.31200 21.98800 zmin,zma (A): -9.772000 44.42900 x,y,z range (A): 49.35000 48.30000 54.20100 scale (grids/A): 1.970443 object centre (A): 16.31000 -2.162001 17.32850 number of atom coordinates read : 2783 total number of charged atoms : 2631 net assigned charge : 3.618024 assigned positive charge : 419.5555 centred at (gu) : 89.31654 91.03970 85.48457 assigned negative charge : -415.9383 centred at (gu) : 89.99359 90.46199 85.61058 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 86724 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23213 grid for indexing accessible points = 1.400000 m= 32195 mr = 61790 m= 5140 mr = 24181 m= 327 mr = 3298 m= 3 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1808 time to turn everything in is 0.7500000 number of dielectric boundary points 35029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 20721 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) : 0.6568145 object centre at (A) : 16.31000 -2.162001 17.32850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1473696E-03 -4.9426060E-02 midg,1,midg; midg,igrid,midg -1.9280450E-02 4.3114327E-02 1,midg,midg; igrid,midg,midg 7.4124232E-02 9.0852450E-04 gauss-seidel spectral radius is 0.9987369 estimated iterations to convergence 223 setup time was (sec) 1.060000 now iterating at: 08:34:50 rms-change max change #iterations 4.682458 190.0179 at 10iterations 2.262208 72.97430 at 20iterations 1.090324 33.15565 at 30iterations 0.5283647 14.41035 at 40iterations 0.2557108 7.322494 at 50iterations 0.1234584 3.823576 at 60iterations 5.9434813E-02 1.736496 at 70iterations 2.8727490E-02 0.8393841 at 80iterations 1.3894696E-02 0.4101982 at 90iterations 6.7327041E-03 0.1987286 at 100iterations 3.2655841E-03 8.6647034E-02 at 110iterations 1.5864148E-03 5.2101135E-02 at 120iterations finished qdiffx linear iterations at : 08:34:59 total time elapsed so far: 9.630000 # loops : 120 mean,max change (kT/e) : 1.5864148E-03 5.2101135E-02 energy calculations done at 9.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.810000 DelPhi exited at 08:34:59 9.814u 0.321s 0:10.43 97.1% 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 08:34:59 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 = 2783 !!! WARNING: TRP 148 has a net charge of -0.2720 !!! WARNING: ASP 292 has a net charge of -0.2720 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.955665 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): -8.365000 40.98500 ymin,ymax (A): -26.31200 21.98800 zmin,zma (A): -9.772000 44.42900 x,y,z range (A): 49.35000 48.30000 54.20100 scale (grids/A): 2.955665 object centre (A): 16.31000 -2.162001 17.32850 number of atom coordinates read : 2783 total number of charged atoms : 2631 net assigned charge : 3.618024 assigned positive charge : 419.5555 centred at (gu) : 88.97475 91.55928 83.22655 assigned negative charge : -415.9383 centred at (gu) : 89.99035 90.69292 83.41577 start vw surface at 0.1700000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 200411 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23213 grid for indexing accessible points = 1.400000 m= 104250 mr = 149235 m= 38206 mr = 86421 m= 9473 mr = 31073 m= 1382 mr = 7170 m= 75 mr = 953 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 6249 time to turn everything in is 2.000000 number of dielectric boundary points 78927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 21012 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) : 1.970443 object centre at (A) : 16.31000 -2.162001 17.32850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2055340 -0.6643677 midg,1,midg; midg,igrid,midg -0.2203145 0.4882331 1,midg,midg; igrid,midg,midg 0.6418059 5.0037865E-02 gauss-seidel spectral radius is 0.9992855 estimated iterations to convergence 295 setup time was (sec) 2.350000 now iterating at: 08:35:02 rms-change max change #iterations 10.79078 568.3300 at 10iterations 6.343863 132.3504 at 20iterations 3.715487 77.72826 at 30iterations 2.184959 41.01537 at 40iterations 1.273815 25.01168 at 50iterations 0.7437397 13.17913 at 60iterations 0.4335050 7.328313 at 70iterations 0.2527821 4.227173 at 80iterations 0.1471528 2.553936 at 90iterations 8.5511699E-02 1.376694 at 100iterations 4.9815618E-02 0.8941154 at 110iterations 2.9049775E-02 0.4943085 at 120iterations 1.6938426E-02 0.3086567 at 130iterations 9.8722931E-03 0.1672382 at 140iterations 5.7826070E-03 0.1047211 at 150iterations 3.4118553E-03 5.7422638E-02 at 160iterations 2.0327850E-03 3.5243988E-02 at 170iterations 1.2346901E-03 2.1986008E-02 at 180iterations finished qdiffx linear iterations at : 08:35:16 total time elapsed so far: 16.75000 # loops : 180 mean,max change (kT/e) : 1.2346901E-03 2.1986008E-02 energy calculations done at 16.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.93000 DelPhi exited at 08:35:17 16.932u 0.308s 0:17.81 96.7% 0+0k 0+0io 0pf+0w