Sat Oct 15 11:29:49 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 15 2011 at 11:29:49 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 423 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6215734 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): -31.30800 17.52900 ymin,ymax (A): -24.03000 22.12900 zmin,zma (A): -12.37100 44.90300 x,y,z range (A): 48.83700 46.15900 57.27400 scale (grids/A): 0.6215734 object centre (A): -6.889501 -0.9504995 16.26600 number of atom coordinates read : 2591 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 88.48747 89.58303 89.64851 assigned negative charge : -387.9385 centred at (gu) : 88.38817 89.63394 89.53668 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6632 nv = 96 ne = 84 npr = 53486 no. pairs analyzed = 53486 no. exposed pairs = 3048 no. arc points = 21707 no. surface atoms = 1019 nbur = 1572 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3731 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 0.3100000 number of dielectric boundary points 3205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2113 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8116 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7990789E-09 1.0263681E-08 midg,1,midg; midg,igrid,midg 7.6051414E-09 -9.3763768E-11 1,midg,midg; igrid,midg,midg -5.0583244E-09 7.3626363E-09 gauss-seidel spectral radius is 0.9865929 estimated iterations to convergence 71 setup time was (sec) 0.6200000 now iterating at: 11:29:50 rms-change max change #iterations 0.1322726 22.40342 at 10iterations 1.2074320E-02 1.932544 at 20iterations 1.1260761E-03 0.1503134 at 30iterations 1.0498826E-04 1.5195847E-02 at 40iterations 1.0106387E-05 1.5525818E-03 at 50iterations finished qdiffx linear iterations at : 11:29:54 total time elapsed so far: 5.270000 # loops : 50 mean,max change (kT/e) : 1.0106387E-05 1.5525818E-03 energy calculations done at 5.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.440000 DelPhi exited at 11:29:55 5.447u 0.466s 0:06.41 92.0% 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 Sat Oct 15 2011 at 11:29:55 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 423 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.864720 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): -31.30800 17.52900 ymin,ymax (A): -24.03000 22.12900 zmin,zma (A): -12.37100 44.90300 x,y,z range (A): 48.83700 46.15900 57.27400 scale (grids/A): 1.864720 object centre (A): -6.889501 -0.9504995 16.26600 number of atom coordinates read : 2591 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 85.46203 88.74863 88.94520 assigned negative charge : -387.9385 centred at (gu) : 85.16428 88.90172 88.61000 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72044 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21707 grid for indexing accessible points = 1.400000 m= 25275 mr = 50436 m= 3544 mr = 18832 m= 160 mr = 2125 m= 4 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 4163 time to turn everything in is 0.6000000 number of dielectric boundary points 29590 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19245 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) : 0.6215734 object centre at (A) : -6.889501 -0.9504995 16.26600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2217108E-02 1.9903669E-02 midg,1,midg; midg,igrid,midg 1.3710469E-02 1.4700348E-04 1,midg,midg; igrid,midg,midg -4.0478781E-03 3.8325645E-02 gauss-seidel spectral radius is 0.9985765 estimated iterations to convergence 210 setup time was (sec) 0.9500000 now iterating at: 11:29:57 rms-change max change #iterations 4.049881 183.2236 at 10iterations 1.867020 62.30013 at 20iterations 0.8585272 29.41142 at 30iterations 0.3957040 15.54079 at 40iterations 0.1823999 5.765316 at 50iterations 8.4147453E-02 2.922485 at 60iterations 3.8914636E-02 1.209040 at 70iterations 1.7955130E-02 0.5884590 at 80iterations 8.2733380E-03 0.2711086 at 90iterations 3.8182442E-03 0.1187096 at 100iterations 1.7579851E-03 5.4925919E-02 at 110iterations 8.1135059E-04 2.5417328E-02 at 120iterations finished qdiffx linear iterations at : 11:30:08 total time elapsed so far: 12.74000 # loops : 120 mean,max change (kT/e) : 8.1135059E-04 2.5417328E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 11:30:09 12.912u 0.537s 0:13.78 97.5% 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 15 2011 at 11:30:09 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 423 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.797081 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): -31.30800 17.52900 ymin,ymax (A): -24.03000 22.12900 zmin,zma (A): -12.37100 44.90300 x,y,z range (A): 48.83700 46.15900 57.27400 scale (grids/A): 2.797081 object centre (A): -6.889501 -0.9504995 16.26600 number of atom coordinates read : 2591 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 83.19296 88.12286 88.41771 assigned negative charge : -387.9385 centred at (gu) : 82.74639 88.35235 87.91499 start vw surface at 0.1200000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 166845 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21707 grid for indexing accessible points = 1.400000 m= 83317 mr = 122057 m= 28615 mr = 68853 m= 6197 mr = 22970 m= 728 mr = 4548 m= 39 mr = 464 m= 0 mr = 11 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 14680 time to turn everything in is 1.560000 number of dielectric boundary points 66838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 19600 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) : 1.864720 object centre at (A) : -6.889501 -0.9504995 16.26600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1269895 0.2165133 midg,1,midg; midg,igrid,midg 0.1566566 -3.9730124E-02 1,midg,midg; igrid,midg,midg -4.1344855E-02 0.5297824 gauss-seidel spectral radius is 0.9992374 estimated iterations to convergence 286 setup time was (sec) 1.940000 now iterating at: 11:30:11 rms-change max change #iterations 9.493654 335.3411 at 10iterations 5.452293 114.3097 at 20iterations 3.116428 65.36988 at 30iterations 1.780034 32.77258 at 40iterations 1.014183 19.49797 at 50iterations 0.5781851 10.50069 at 60iterations 0.3299193 6.440104 at 70iterations 0.1878297 3.396698 at 80iterations 0.1069859 2.097027 at 90iterations 6.0781639E-02 1.164112 at 100iterations 3.4658805E-02 0.6551702 at 110iterations 1.9737035E-02 0.3661838 at 120iterations 1.1246813E-02 0.2158778 at 130iterations 6.3974387E-03 0.1252060 at 140iterations 3.6457940E-03 6.3526154E-02 at 150iterations 2.0730486E-03 4.1583061E-02 at 160iterations 1.1831067E-03 2.1385193E-02 at 170iterations 6.7526958E-04 1.2148857E-02 at 180iterations finished qdiffx linear iterations at : 11:30:31 total time elapsed so far: 21.42000 # loops : 180 mean,max change (kT/e) : 6.7526958E-04 1.2148857E-02 energy calculations done at 21.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.59000 DelPhi exited at 11:30:31 21.593u 0.562s 0:22.41 98.8% 0+0k 0+0io 0pf+0w