Tue Oct 11 08:17:41 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 08:17:41 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 = 2767 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: 0.6354533 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): -5.050000 50.97300 ymin,ymax (A): -16.25000 29.52500 zmin,zma (A): 57.27500 109.4010 x,y,z range (A): 56.02300 45.77500 52.12600 scale (grids/A): 0.6354533 object centre (A): 22.96150 6.637500 83.33800 number of atom coordinates read : 2767 total number of charged atoms : 2623 net assigned charge : 5.500018 assigned positive charge : 418.0574 centred at (gu) : 90.02935 90.21194 89.43759 assigned negative charge : -412.5582 centred at (gu) : 90.27004 90.12986 89.48164 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7513 nv = 96 ne = 84 npr = 55976 no. pairs analyzed = 55976 no. exposed pairs = 3255 no. arc points = 23057 no. surface atoms = 1102 nbur = 1665 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 4282 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 109 time to turn everything in is 0.2200000 number of dielectric boundary points 3556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2287 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9013 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3324473E-08 1.9619000E-09 midg,1,midg; midg,igrid,midg -1.9401538E-09 1.6665735E-08 1,midg,midg; igrid,midg,midg 3.2480674E-08 -2.0178588E-08 gauss-seidel spectral radius is 0.9871838 estimated iterations to convergence 72 setup time was (sec) 0.4100000 now iterating at: 08:17:42 rms-change max change #iterations 0.1450440 22.76357 at 10iterations 1.4717855E-02 1.979889 at 20iterations 2.0494538E-03 0.3714790 at 30iterations 5.1543838E-04 0.1102753 at 40iterations 1.5343970E-04 3.4431458E-02 at 50iterations finished qdiffx linear iterations at : 08:17:45 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.5343970E-04 3.4431458E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 08:17:46 3.463u 0.156s 0:04.40 82.0% 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 08:17:46 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 = 2767 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: 1.906360 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): -5.050000 50.97300 ymin,ymax (A): -16.25000 29.52500 zmin,zma (A): 57.27500 109.4010 x,y,z range (A): 56.02300 45.77500 52.12600 scale (grids/A): 1.906360 object centre (A): 22.96150 6.637500 83.33800 number of atom coordinates read : 2767 total number of charged atoms : 2623 net assigned charge : 5.500018 assigned positive charge : 418.0574 centred at (gu) : 90.08744 90.63510 88.31223 assigned negative charge : -412.5582 centred at (gu) : 90.80976 90.38923 88.44463 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 81136 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23057 grid for indexing accessible points = 1.400000 m= 29490 mr = 57342 m= 4613 mr = 22235 m= 257 mr = 3060 m= 4 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 5406 time to turn everything in is 0.4100000 number of dielectric boundary points 32760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20627 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) : 0.6354533 object centre at (A) : 22.96150 6.637500 83.33800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7123979E-03 6.6095646E-03 midg,1,midg; midg,igrid,midg 1.2449752E-02 2.0968851E-02 1,midg,midg; igrid,midg,midg 4.7611441E-02 -3.5071157E-02 gauss-seidel spectral radius is 0.9986507 estimated iterations to convergence 216 setup time was (sec) 0.6200000 now iterating at: 08:17:47 rms-change max change #iterations 4.389730 176.7133 at 10iterations 2.063479 66.45597 at 20iterations 0.9682323 29.91058 at 30iterations 0.4556344 14.25273 at 40iterations 0.2149030 6.383889 at 50iterations 0.1010534 3.166443 at 60iterations 4.7565173E-02 1.445635 at 70iterations 2.2654517E-02 0.7682118 at 80iterations 1.0752006E-02 0.3778572 at 90iterations 5.1654195E-03 0.1776505 at 100iterations 2.5439532E-03 8.5243225E-02 at 110iterations 1.3120802E-03 4.7962189E-02 at 120iterations finished qdiffx linear iterations at : 08:17:54 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 1.3120802E-03 4.7962189E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 08:17:54 7.911u 0.196s 0:08.42 96.1% 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 08:17:54 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 = 2767 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.859540 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): -5.050000 50.97300 ymin,ymax (A): -16.25000 29.52500 zmin,zma (A): 57.27500 109.4010 x,y,z range (A): 56.02300 45.77500 52.12600 scale (grids/A): 2.859540 object centre (A): 22.96150 6.637500 83.33800 number of atom coordinates read : 2767 total number of charged atoms : 2623 net assigned charge : 5.500018 assigned positive charge : 418.0574 centred at (gu) : 90.13097 90.95254 87.46826 assigned negative charge : -412.5582 centred at (gu) : 91.21455 90.58384 87.66680 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 187949 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23057 grid for indexing accessible points = 1.400000 m= 95729 mr = 138822 m= 34598 mr = 79523 m= 8249 mr = 28355 m= 1166 mr = 6477 m= 49 mr = 792 m= 0 mr = 19 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 17357 time to turn everything in is 1.000000 number of dielectric boundary points 73752 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 20982 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) : 1.906360 object centre at (A) : 22.96150 6.637500 83.33800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2255639E-02 1.1622900E-02 midg,1,midg; midg,igrid,midg 0.2003505 0.2279161 1,midg,midg; igrid,midg,midg 0.5741948 -0.2329145 gauss-seidel spectral radius is 0.9992589 estimated iterations to convergence 290 setup time was (sec) 1.240000 now iterating at: 08:17:56 rms-change max change #iterations 10.19011 356.0683 at 10iterations 5.913884 116.3867 at 20iterations 3.418749 63.62770 at 30iterations 1.968517 35.52409 at 40iterations 1.131734 19.36615 at 50iterations 0.6522536 11.83471 at 60iterations 0.3748991 6.606287 at 70iterations 0.2160396 4.137704 at 80iterations 0.1241299 2.171658 at 90iterations 7.1271747E-02 1.290710 at 100iterations 4.1012261E-02 0.7424049 at 110iterations 2.3566555E-02 0.4247632 at 120iterations 1.3594554E-02 0.2354717 at 130iterations 7.8656981E-03 0.1301546 at 140iterations 4.5615342E-03 8.4373474E-02 at 150iterations 2.6795990E-03 5.2001953E-02 at 160iterations 1.6028595E-03 3.6342621E-02 at 170iterations 9.9083572E-04 2.3372650E-02 at 180iterations finished qdiffx linear iterations at : 08:18:07 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 9.9083572E-04 2.3372650E-02 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 08:18:08 12.603u 0.228s 0:13.36 95.9% 0+0k 0+0io 0pf+0w