Sat Oct 8 11:39:32 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 11:39:32 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2923 !!! WARNING: HIT 134 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5365162 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): -6.563000 46.56100 ymin,ymax (A): -27.67300 38.68100 zmin,zma (A): -18.07200 30.23500 x,y,z range (A): 53.12400 66.35400 48.30700 scale (grids/A): 0.5365162 object centre (A): 19.99900 5.504000 6.081500 number of atom coordinates read : 2923 total number of charged atoms : 2765 net assigned charge : -9.985991 assigned positive charge : 434.4969 centred at (gu) : 88.90253 88.54908 90.22878 assigned negative charge : -444.4839 centred at (gu) : 88.97195 88.67149 90.26916 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 5505 nv = 96 ne = 84 npr = 58091 no. pairs analyzed = 58091 no. exposed pairs = 3988 no. arc points = 28446 no. surface atoms = 1347 nbur = 1576 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 226 mr = 2662 m= 0 mr = 9 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3060 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2787 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 7174 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3830621E-10 -6.6119882E-10 midg,1,midg; midg,igrid,midg 1.8453888E-10 -7.0509548E-10 1,midg,midg; igrid,midg,midg -1.5088031E-10 -5.7967553E-10 gauss-seidel spectral radius is 0.9821005 estimated iterations to convergence 62 setup time was (sec) 0.7000000 now iterating at: 11:39:33 rms-change max change #iterations 6.3439488E-02 13.01497 at 10iterations 4.1173273E-03 0.8123479 at 20iterations 2.6601294E-04 4.6871185E-02 at 30iterations 2.0086301E-05 3.6048889E-03 at 40iterations 2.3811422E-06 5.2356720E-04 at 50iterations finished qdiffx linear iterations at : 11:39:36 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 2.3811422E-06 5.2356720E-04 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 11:39:37 4.068u 0.183s 0:04.80 88.3% 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 11:39:37 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2923 !!! WARNING: HIT 134 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.609549 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): -6.563000 46.56100 ymin,ymax (A): -27.67300 38.68100 zmin,zma (A): -18.07200 30.23500 x,y,z range (A): 53.12400 66.35400 48.30700 scale (grids/A): 1.609549 object centre (A): 19.99900 5.504000 6.081500 number of atom coordinates read : 2923 total number of charged atoms : 2765 net assigned charge : -9.985991 assigned positive charge : 434.4969 centred at (gu) : 86.70654 85.64616 90.68542 assigned negative charge : -444.4839 centred at (gu) : 86.91551 86.01395 90.80688 start vw surface at 0.2600000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 61026 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28446 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17352 mr = 39541 m= 1563 mr = 11246 m= 38 mr = 623 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 28569 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 315 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 21093 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) : 0.5365162 object centre at (A) : 19.99900 5.504000 6.081500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7888136E-03 -7.5761736E-03 midg,1,midg; midg,igrid,midg -3.5685895E-05 -1.7713916E-02 1,midg,midg; igrid,midg,midg 1.6033390E-03 -8.5981665E-03 gauss-seidel spectral radius is 0.9981315 estimated iterations to convergence 184 setup time was (sec) 1.010000 now iterating at: 11:39:38 rms-change max change #iterations 3.231101 149.6296 at 10iterations 1.320991 53.47445 at 20iterations 0.5448586 22.44231 at 30iterations 0.2226916 8.256353 at 40iterations 9.1506720E-02 3.425770 at 50iterations 3.7828699E-02 1.409519 at 60iterations 1.5526336E-02 0.6167526 at 70iterations 6.3851066E-03 0.2209816 at 80iterations 2.6300445E-03 0.1064720 at 90iterations 1.0824411E-03 5.3136826E-02 at 100iterations 4.4485994E-04 1.5863419E-02 at 110iterations 1.8355560E-04 7.2107315E-03 at 120iterations finished qdiffx linear iterations at : 11:39:46 total time elapsed so far: 8.880000 # loops : 120 mean,max change (kT/e) : 1.8355560E-04 7.2107315E-03 energy calculations done at 8.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.120000 DelPhi exited at 11:39:47 9.125u 0.197s 0:09.84 94.6% 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 11:39:47 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2923 !!! WARNING: HIT 134 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.414323 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): -6.563000 46.56100 ymin,ymax (A): -27.67300 38.68100 zmin,zma (A): -18.07200 30.23500 x,y,z range (A): 53.12400 66.35400 48.30700 scale (grids/A): 2.414323 object centre (A): 19.99900 5.504000 6.081500 number of atom coordinates read : 2923 total number of charged atoms : 2765 net assigned charge : -9.985991 assigned positive charge : 434.4969 centred at (gu) : 85.05975 83.46928 91.02777 assigned negative charge : -444.4839 centred at (gu) : 85.37306 84.02084 91.21023 start vw surface at 0.2400000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 141821 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28446 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 60967 mr = 97507 m= 15937 mr = 46664 m= 2219 mr = 11254 m= 137 mr = 1235 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.370000 number of dielectric boundary points 64352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 22088 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) : 1.609549 object centre at (A) : 19.99900 5.504000 6.081500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6734567E-02 -9.8413296E-02 midg,1,midg; midg,igrid,midg 0.3366382 -0.2519770 1,midg,midg; igrid,midg,midg 3.3595212E-02 -0.1185606 gauss-seidel spectral radius is 0.9991220 estimated iterations to convergence 267 setup time was (sec) 1.740000 now iterating at: 11:39:49 rms-change max change #iterations 8.549437 294.1923 at 10iterations 4.811180 138.4488 at 20iterations 2.690598 97.88451 at 30iterations 1.492211 36.23489 at 40iterations 0.8235694 20.94396 at 50iterations 0.4547938 10.37272 at 60iterations 0.2506832 6.556953 at 70iterations 0.1376683 3.464222 at 80iterations 7.5438596E-02 1.567688 at 90iterations 4.1338548E-02 0.9296265 at 100iterations 2.2610262E-02 0.5059891 at 110iterations 1.2360941E-02 0.2769003 at 120iterations 6.7768283E-03 0.1590667 at 130iterations 3.7005318E-03 7.8266621E-02 at 140iterations 2.0249086E-03 4.4635773E-02 at 150iterations 1.1091587E-03 2.5623322E-02 at 160iterations 6.0719607E-04 1.2836456E-02 at 170iterations 3.3282943E-04 7.3928833E-03 at 180iterations finished qdiffx linear iterations at : 11:40:01 total time elapsed so far: 13.67000 # loops : 180 mean,max change (kT/e) : 3.3282943E-04 7.3928833E-03 energy calculations done at 13.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.90000 DelPhi exited at 11:40:01 13.897u 0.208s 0:14.54 96.9% 0+0k 0+0io 0pf+0w