Tue Oct 11 03:22:04 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 Tue Oct 11 2011 at 03:22:04 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3105 !!! WARNING: GLM 19 has a net charge of -0.0940 !!! WARNING: SEP 84 has a net charge of -0.4750 !!! WARNING: ASP 165 has a net charge of -0.2720 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: 0.5927603 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): 53.85100 113.9090 ymin,ymax (A): 7.2000027E-02 43.82300 zmin,zma (A): -65.17200 -10.53700 x,y,z range (A): 60.05801 43.75100 54.63499 scale (grids/A): 0.5927603 object centre (A): 83.88000 21.94750 -37.85450 number of atom coordinates read : 3105 total number of charged atoms : 2962 net assigned charge : -4.840959 assigned positive charge : 463.3731 centred at (gu) : 91.54290 90.37842 88.04762 assigned negative charge : -468.2150 centred at (gu) : 91.53040 90.39822 88.00842 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7077 nv = 96 ne = 84 npr = 64712 no. pairs analyzed = 64712 no. exposed pairs = 3807 no. arc points = 26839 no. surface atoms = 1293 nbur = 1812 mkacc time = 0.1700000 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 = 1.484000 m= 381 mr = 3888 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.3400000 number of dielectric boundary points 3534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2749 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9033 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6506941E-09 -1.7497341E-10 midg,1,midg; midg,igrid,midg -8.3866558E-10 -2.4916125E-09 1,midg,midg; igrid,midg,midg -1.4422719E-09 -1.6294108E-09 gauss-seidel spectral radius is 0.9853113 estimated iterations to convergence 68 setup time was (sec) 0.6200000 now iterating at: 03:22:05 rms-change max change #iterations 0.1171269 17.34982 at 10iterations 9.7319027E-03 1.554481 at 20iterations 8.3978154E-04 0.1302252 at 30iterations 1.0861640E-04 1.6159058E-02 at 40iterations 2.7754275E-05 4.6737194E-03 at 50iterations finished qdiffx linear iterations at : 03:22:09 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 2.7754275E-05 4.6737194E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 03:22:09 4.471u 0.384s 0:05.27 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 Tue Oct 11 2011 at 03:22:09 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3105 !!! WARNING: GLM 19 has a net charge of -0.0940 !!! WARNING: SEP 84 has a net charge of -0.4750 !!! WARNING: ASP 165 has a net charge of -0.2720 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: 1.778281 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): 53.85100 113.9090 ymin,ymax (A): 7.2000027E-02 43.82300 zmin,zma (A): -65.17200 -10.53700 x,y,z range (A): 60.05801 43.75100 54.63499 scale (grids/A): 1.778281 object centre (A): 83.88000 21.94750 -37.85450 number of atom coordinates read : 3105 total number of charged atoms : 2962 net assigned charge : -4.840959 assigned positive charge : 463.3731 centred at (gu) : 94.62814 91.13441 84.14206 assigned negative charge : -468.2150 centred at (gu) : 94.59081 91.19431 84.02509 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26839 grid for indexing accessible points = 1.400000 m= 28107 mr = 51835 m= 4370 mr = 21041 m= 179 mr = 2660 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1456 time to turn everything in is 0.6300000 number of dielectric boundary points 32703 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 231 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 23066 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) : 0.5927603 object centre at (A) : 83.88000 21.94750 -37.85450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3138635E-02 1.7117430E-02 midg,1,midg; midg,igrid,midg -4.1016075E-03 -1.0264618E-02 1,midg,midg; igrid,midg,midg -1.0095798E-02 -4.0347621E-02 gauss-seidel spectral radius is 0.9984777 estimated iterations to convergence 203 setup time was (sec) 0.9200000 now iterating at: 03:22:11 rms-change max change #iterations 4.103274 160.1371 at 10iterations 1.830134 62.56245 at 20iterations 0.8202146 29.12251 at 30iterations 0.3690695 11.74030 at 40iterations 0.1653183 5.310988 at 50iterations 7.4285701E-02 2.482529 at 60iterations 3.3383001E-02 1.146702 at 70iterations 1.5018432E-02 0.4757996 at 80iterations 6.7722495E-03 0.2123032 at 90iterations 3.0720518E-03 9.7828865E-02 at 100iterations 1.4117504E-03 4.7210693E-02 at 110iterations 6.6564529E-04 2.6473045E-02 at 120iterations finished qdiffx linear iterations at : 03:22:20 total time elapsed so far: 10.47000 # loops : 120 mean,max change (kT/e) : 6.6564529E-04 2.6473045E-02 energy calculations done at 10.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.63000 DelPhi exited at 03:22:21 10.636u 0.442s 0:11.39 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 03:22:21 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3105 !!! WARNING: GLM 19 has a net charge of -0.0940 !!! WARNING: SEP 84 has a net charge of -0.4750 !!! WARNING: ASP 165 has a net charge of -0.2720 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: 2.667421 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): 53.85100 113.9090 ymin,ymax (A): 7.2000027E-02 43.82300 zmin,zma (A): -65.17200 -10.53700 x,y,z range (A): 60.05801 43.75100 54.63499 scale (grids/A): 2.667421 object centre (A): 83.88000 21.94750 -37.85450 number of atom coordinates read : 3105 total number of charged atoms : 2962 net assigned charge : -4.840959 assigned positive charge : 463.3731 centred at (gu) : 96.94202 91.70123 81.21278 assigned negative charge : -468.2150 centred at (gu) : 96.88618 91.79128 81.03748 start vw surface at 0.1200000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 174831 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26839 grid for indexing accessible points = 1.400000 m= 89449 mr = 125935 m= 33973 mr = 73222 m= 7646 mr = 27694 m= 897 mr = 5655 m= 36 mr = 523 m= 0 mr = 7 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 5104 time to turn everything in is 1.620000 number of dielectric boundary points 73796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 23687 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) : 1.778281 object centre at (A) : 83.88000 21.94750 -37.85450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4149279 0.1487358 midg,1,midg; midg,igrid,midg -4.1680429E-02 -0.1144354 1,midg,midg; igrid,midg,midg -0.1173130 -0.8502476 gauss-seidel spectral radius is 0.9992272 estimated iterations to convergence 284 setup time was (sec) 2.030000 now iterating at: 03:22:23 rms-change max change #iterations 9.975835 299.1149 at 10iterations 5.769753 114.6306 at 20iterations 3.316447 70.91178 at 30iterations 1.892439 35.79467 at 40iterations 1.081447 20.54761 at 50iterations 0.6172150 12.97077 at 60iterations 0.3513418 7.158499 at 70iterations 0.1999664 4.116799 at 80iterations 0.1137630 2.086006 at 90iterations 6.4580180E-02 1.161630 at 100iterations 3.6789872E-02 0.6916461 at 110iterations 2.0909807E-02 0.3936691 at 120iterations 1.1888287E-02 0.2245305 at 130iterations 6.7678532E-03 0.1315193 at 140iterations 3.8768642E-03 7.6385498E-02 at 150iterations 2.2280659E-03 3.8767278E-02 at 160iterations 1.2983942E-03 2.5535583E-02 at 170iterations 7.7258691E-04 1.6234875E-02 at 180iterations finished qdiffx linear iterations at : 03:22:39 total time elapsed so far: 18.00000 # loops : 180 mean,max change (kT/e) : 7.7258691E-04 1.6234875E-02 energy calculations done at 18.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.17000 DelPhi exited at 03:22:40 18.172u 0.471s 0:18.96 98.3% 0+0k 0+0io 0pf+0w