Tue Oct 11 07:29:53 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 07:29:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3190 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: 0.5963448 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): 0.5619999 48.86500 ymin,ymax (A): -7.777000 49.24900 zmin,zma (A): 1.089000 60.78600 x,y,z range (A): 48.30300 57.02600 59.69700 scale (grids/A): 0.5963448 object centre (A): 24.71350 20.73600 30.93750 number of atom coordinates read : 3190 total number of charged atoms : 3048 net assigned charge : -0.9999906 assigned positive charge : 480.4119 centred at (gu) : 89.67114 89.20543 90.97727 assigned negative charge : -481.4130 centred at (gu) : 89.59970 89.12055 90.93511 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7530 nv = 96 ne = 84 npr = 65220 no. pairs analyzed = 65220 no. exposed pairs = 3794 no. arc points = 25915 no. surface atoms = 1287 nbur = 1903 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 362 mr = 4387 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.2600000 number of dielectric boundary points 3473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2525 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9413 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6491747E-09 1.6869075E-09 midg,1,midg; midg,igrid,midg -4.5851727E-09 2.5227054E-09 1,midg,midg; igrid,midg,midg -3.5175571E-09 2.3179707E-09 gauss-seidel spectral radius is 0.9854931 estimated iterations to convergence 68 setup time was (sec) 0.4400000 now iterating at: 07:29:53 rms-change max change #iterations 0.1168418 16.39119 at 10iterations 1.0600463E-02 1.524185 at 20iterations 9.5426507E-04 0.1315327 at 30iterations 1.3305909E-04 2.2327423E-02 at 40iterations 2.4143939E-05 4.6215057E-03 at 50iterations finished qdiffx linear iterations at : 07:29:56 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 2.4143939E-05 4.6215057E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 07:29:57 3.482u 0.168s 0:04.06 89.6% 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 Tue Oct 11 2011 at 07:29:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3190 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: 1.789035 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): 0.5619999 48.86500 ymin,ymax (A): -7.777000 49.24900 zmin,zma (A): 1.089000 60.78600 x,y,z range (A): 48.30300 57.02600 59.69700 scale (grids/A): 1.789035 object centre (A): 24.71350 20.73600 30.93750 number of atom coordinates read : 3190 total number of charged atoms : 3048 net assigned charge : -0.9999906 assigned positive charge : 480.4119 centred at (gu) : 89.01286 87.61559 92.93101 assigned negative charge : -481.4130 centred at (gu) : 88.79868 87.36137 92.80502 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82622 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25915 grid for indexing accessible points = 1.400000 m= 29672 mr = 59452 m= 4061 mr = 22422 m= 130 mr = 2501 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1635 time to turn everything in is 0.4100000 number of dielectric boundary points 32071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 213 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 23783 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) : 0.5963448 object centre at (A) : 24.71350 20.73600 30.93750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5397605E-03 5.2559501E-03 midg,1,midg; midg,igrid,midg -2.0895608E-02 1.0256783E-02 1,midg,midg; igrid,midg,midg -1.4106789E-02 1.0244254E-03 gauss-seidel spectral radius is 0.9985148 estimated iterations to convergence 206 setup time was (sec) 0.6400000 now iterating at: 07:29:58 rms-change max change #iterations 4.231735 188.5579 at 10iterations 1.917347 71.58696 at 20iterations 0.8717120 27.63708 at 30iterations 0.3964630 12.58304 at 40iterations 0.1796406 5.554095 at 50iterations 8.1739202E-02 2.794401 at 60iterations 3.7289351E-02 1.110115 at 70iterations 1.6938930E-02 0.5413642 at 80iterations 7.7062817E-03 0.2334251 at 90iterations 3.5230878E-03 0.1081238 at 100iterations 1.6171192E-03 5.7155609E-02 at 110iterations 7.4118853E-04 2.3849487E-02 at 120iterations finished qdiffx linear iterations at : 07:30:05 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 7.4118853E-04 2.3849487E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 07:30:06 7.962u 0.198s 0:08.75 93.1% 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 07:30:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.683552 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): 0.5619999 48.86500 ymin,ymax (A): -7.777000 49.24900 zmin,zma (A): 1.089000 60.78600 x,y,z range (A): 48.30300 57.02600 59.69700 scale (grids/A): 2.683552 object centre (A): 24.71350 20.73600 30.93750 number of atom coordinates read : 3190 total number of charged atoms : 3048 net assigned charge : -0.9999906 assigned positive charge : 480.4119 centred at (gu) : 88.51926 86.42328 94.39648 assigned negative charge : -481.4130 centred at (gu) : 88.19788 86.04199 94.20745 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 191466 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25915 grid for indexing accessible points = 1.400000 m= 98001 mr = 143379 m= 33381 mr = 81660 m= 6930 mr = 27257 m= 707 mr = 5268 m= 12 mr = 434 m= 0 mr = 3 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 5554 time to turn everything in is 1.000000 number of dielectric boundary points 72496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 24382 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) : 1.789035 object centre at (A) : 24.71350 20.73600 30.93750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2845576 -0.1963279 midg,1,midg; midg,igrid,midg -0.3894306 0.1159465 1,midg,midg; igrid,midg,midg -0.1523113 5.6602561E-04 gauss-seidel spectral radius is 0.9992337 estimated iterations to convergence 285 setup time was (sec) 1.230000 now iterating at: 07:30:07 rms-change max change #iterations 10.10189 261.5649 at 10iterations 5.822517 126.0845 at 20iterations 3.346205 64.53875 at 30iterations 1.910521 37.14603 at 40iterations 1.093046 20.29677 at 50iterations 0.6240503 10.88911 at 60iterations 0.3559414 6.711573 at 70iterations 0.2028856 4.128639 at 80iterations 0.1157494 1.977379 at 90iterations 6.5919675E-02 1.101437 at 100iterations 3.7540700E-02 0.6730909 at 110iterations 2.1347389E-02 0.3988533 at 120iterations 1.2167182E-02 0.2252731 at 130iterations 6.9272374E-03 0.1253853 at 140iterations 3.9551891E-03 7.0442200E-02 at 150iterations 2.2613069E-03 3.7902832E-02 at 160iterations 1.2908584E-03 2.3258209E-02 at 170iterations 7.4014178E-04 1.3089180E-02 at 180iterations finished qdiffx linear iterations at : 07:30:18 total time elapsed so far: 12.42000 # loops : 180 mean,max change (kT/e) : 7.4014178E-04 1.3089180E-02 energy calculations done at 12.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 07:30:19 12.556u 0.206s 0:13.40 95.1% 0+0k 0+0io 0pf+0w