Sat Oct 8 11:34:24 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 11:34:24 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4464 !!! WARNING: HIR 440 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5793139 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): -25.54500 34.23700 ymin,ymax (A): 37.75400 99.20600 zmin,zma (A): 30.34500 89.72200 x,y,z range (A): 59.78201 61.45200 59.37700 scale (grids/A): 0.5793139 object centre (A): 4.346002 68.48000 60.03350 number of atom coordinates read : 4464 total number of charged atoms : 4304 net assigned charge : -2.485960 assigned positive charge : 672.9664 centred at (gu) : 90.44959 87.77935 88.55413 assigned negative charge : -675.4552 centred at (gu) : 90.36404 87.86246 88.65063 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 9564 nv = 96 ne = 84 npr = 95058 no. pairs analyzed = 95058 no. exposed pairs = 4887 no. arc points = 33253 no. surface atoms = 1663 nbur = 2801 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 = 1.484000 m= 440 mr = 5677 m= 0 mr = 28 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 66 time to turn everything in is 0.3000000 number of dielectric boundary points 4299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3515 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 12586 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4694223E-09 -2.7204983E-09 midg,1,midg; midg,igrid,midg 3.4729175E-09 -2.0101829E-09 1,midg,midg; igrid,midg,midg -3.1102416E-09 2.3342921E-09 gauss-seidel spectral radius is 0.9847236 estimated iterations to convergence 66 setup time was (sec) 0.5000000 now iterating at: 11:34:25 rms-change max change #iterations 0.1234229 16.07802 at 10iterations 9.8894499E-03 1.667225 at 20iterations 9.4046531E-04 0.1039429 at 30iterations 1.6691738E-04 2.1747589E-02 at 40iterations 5.5196906E-05 7.5356662E-03 at 50iterations finished qdiffx linear iterations at : 11:34:28 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 5.5196906E-05 7.5356662E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 11:34:28 3.564u 0.185s 0:04.20 89.0% 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 8 2011 at 11:34:28 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4464 !!! WARNING: HIR 440 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.737942 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): -25.54500 34.23700 ymin,ymax (A): 37.75400 99.20600 zmin,zma (A): 30.34500 89.72200 x,y,z range (A): 59.78201 61.45200 59.37700 scale (grids/A): 1.737942 object centre (A): 4.346002 68.48000 60.03350 number of atom coordinates read : 4464 total number of charged atoms : 4304 net assigned charge : -2.485960 assigned positive charge : 672.9664 centred at (gu) : 91.34758 83.33695 85.66122 assigned negative charge : -675.4552 centred at (gu) : 91.09165 83.58710 85.95124 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 106133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33253 grid for indexing accessible points = 1.400000 m= 36176 mr = 77707 m= 4727 mr = 26919 m= 206 mr = 2965 m= 0 mr = 53 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 4983 time to turn everything in is 0.5000000 number of dielectric boundary points 39598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 324 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 33368 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) : 0.5793139 object centre at (A) : 4.346002 68.48000 60.03350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0984529E-03 -2.7476566E-02 midg,1,midg; midg,igrid,midg 4.6941206E-02 6.8036625E-03 1,midg,midg; igrid,midg,midg -7.9702893E-03 3.7083618E-02 gauss-seidel spectral radius is 0.9985214 estimated iterations to convergence 206 setup time was (sec) 0.7500000 now iterating at: 11:34:29 rms-change max change #iterations 4.839425 184.6812 at 10iterations 2.199888 69.67786 at 20iterations 1.000623 31.10636 at 30iterations 0.4554685 12.98428 at 40iterations 0.2077034 5.455238 at 50iterations 9.4468631E-02 2.542779 at 60iterations 4.3080706E-02 1.133330 at 70iterations 1.9633522E-02 0.5003290 at 80iterations 8.9423908E-03 0.2518024 at 90iterations 4.0975851E-03 0.1210027 at 100iterations 1.8790159E-03 5.2520752E-02 at 110iterations 8.7459822E-04 2.5178909E-02 at 120iterations finished qdiffx linear iterations at : 11:34:37 total time elapsed so far: 8.120000 # loops : 120 mean,max change (kT/e) : 8.7459822E-04 2.5178909E-02 energy calculations done at 8.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.260000 DelPhi exited at 11:34:38 8.258u 0.196s 0:09.22 91.5% 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 8 2011 at 11:34:38 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4464 !!! WARNING: HIR 440 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.606913 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): -25.54500 34.23700 ymin,ymax (A): 37.75400 99.20600 zmin,zma (A): 30.34500 89.72200 x,y,z range (A): 59.78201 61.45200 59.37700 scale (grids/A): 2.606913 object centre (A): 4.346002 68.48000 60.03350 number of atom coordinates read : 4464 total number of charged atoms : 4304 net assigned charge : -2.485960 assigned positive charge : 672.9664 centred at (gu) : 92.02104 80.00505 83.49161 assigned negative charge : -675.4552 centred at (gu) : 91.63718 80.38056 83.92678 start vw surface at 0.1200000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 247096 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33253 grid for indexing accessible points = 1.400000 m= 122513 mr = 188505 m= 39101 mr = 101607 m= 8204 mr = 31559 m= 913 mr = 6232 m= 27 mr = 602 m= 0 mr = 2 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 16435 time to turn everything in is 1.270000 number of dielectric boundary points 89347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 34425 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) : 1.737942 object centre at (A) : 4.346002 68.48000 60.03350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1467604 -0.3160259 midg,1,midg; midg,igrid,midg 0.6480927 0.1639365 1,midg,midg; igrid,midg,midg -0.1942093 0.3912428 gauss-seidel spectral radius is 0.9992539 estimated iterations to convergence 289 setup time was (sec) 1.520000 now iterating at: 11:34:39 rms-change max change #iterations 11.78138 291.4709 at 10iterations 6.877016 158.2446 at 20iterations 3.991265 66.33475 at 30iterations 2.314091 41.55825 at 40iterations 1.333246 21.73616 at 50iterations 0.7700717 12.92612 at 60iterations 0.4446447 7.582037 at 70iterations 0.2554708 4.060228 at 80iterations 0.1470330 2.423034 at 90iterations 8.4438689E-02 1.362806 at 100iterations 4.8557665E-02 0.8100777 at 110iterations 2.7898474E-02 0.4258126 at 120iterations 1.6022528E-02 0.2579398 at 130iterations 9.2445826E-03 0.1418781 at 140iterations 5.3126556E-03 8.1497192E-02 at 150iterations 3.0698720E-03 4.9423218E-02 at 160iterations 1.7823203E-03 2.8259277E-02 at 170iterations 1.0449527E-03 1.9129276E-02 at 180iterations finished qdiffx linear iterations at : 11:34:52 total time elapsed so far: 13.71000 # loops : 180 mean,max change (kT/e) : 1.0449527E-03 1.9129276E-02 energy calculations done at 13.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.84000 DelPhi exited at 11:34:52 13.842u 0.246s 0:14.66 96.0% 0+0k 0+0io 0pf+0w