Tue Oct 11 08:06:47 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 08:06:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3037 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5528036 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): 9.515000 72.47100 ymin,ymax (A): -0.9660000 63.43300 zmin,zma (A): -4.963000 41.90500 x,y,z range (A): 62.95600 64.39900 46.86800 scale (grids/A): 0.5528036 object centre (A): 40.99300 31.23350 18.47100 number of atom coordinates read : 3037 total number of charged atoms : 2890 net assigned charge : 8.500035 assigned positive charge : 451.7968 centred at (gu) : 90.37149 90.90491 87.99235 assigned negative charge : -443.2980 centred at (gu) : 90.56266 90.94537 87.87978 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6226 nv = 96 ne = 84 npr = 57498 no. pairs analyzed = 57498 no. exposed pairs = 4245 no. arc points = 31066 no. surface atoms = 1428 nbur = 1609 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 = 1.540000 m= 276 mr = 2893 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3146 ## 419 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3827331E-10 1.0224902E-09 midg,1,midg; midg,igrid,midg 8.5305846E-10 4.6095500E-10 1,midg,midg; igrid,midg,midg 2.1001183E-09 -1.0333912E-09 gauss-seidel spectral radius is 0.9831460 estimated iterations to convergence 63 setup time was (sec) 0.6500000 now iterating at: 08:06:48 rms-change max change #iterations 7.7331603E-02 13.23756 at 10iterations 5.2972478E-03 0.7979212 at 20iterations 3.6014724E-04 6.7302704E-02 at 30iterations 2.6194853E-05 3.8146973E-03 at 40iterations 2.1080857E-06 2.8991699E-04 at 50iterations finished qdiffx linear iterations at : 08:06:51 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 2.1080857E-06 2.8991699E-04 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 08:06:52 4.113u 0.255s 0:04.71 92.5% 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 Tue Oct 11 2011 at 08:06:52 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 = 3037 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.658411 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): 9.515000 72.47100 ymin,ymax (A): -0.9660000 63.43300 zmin,zma (A): -4.963000 41.90500 x,y,z range (A): 62.95600 64.39900 46.86800 scale (grids/A): 1.658411 object centre (A): 40.99300 31.23350 18.47100 number of atom coordinates read : 3037 total number of charged atoms : 2890 net assigned charge : 8.500035 assigned positive charge : 451.7968 centred at (gu) : 91.11342 92.71400 83.97626 assigned negative charge : -443.2980 centred at (gu) : 91.68772 92.83553 83.63900 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 68367 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31066 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20200 mr = 43353 m= 2085 mr = 13134 m= 54 mr = 910 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 423 time to turn everything in is 0.6000000 number of dielectric boundary points 33308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 354 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 22140 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) : 0.5528036 object centre at (A) : 40.99300 31.23350 18.47100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3682602E-03 7.1629062E-03 midg,1,midg; midg,igrid,midg -2.0991338E-03 -1.0112261E-02 1,midg,midg; igrid,midg,midg 2.6928714E-02 -5.9643830E-03 gauss-seidel spectral radius is 0.9982582 estimated iterations to convergence 190 setup time was (sec) 0.8900000 now iterating at: 08:06:53 rms-change max change #iterations 3.419524 189.1488 at 10iterations 1.438263 56.80768 at 20iterations 0.6078043 21.49688 at 30iterations 0.2571492 9.068461 at 40iterations 0.1086367 4.100449 at 50iterations 4.5963112E-02 1.662076 at 60iterations 1.9402651E-02 0.6535153 at 70iterations 8.2604950E-03 0.3158822 at 80iterations 3.4775299E-03 0.1301947 at 90iterations 1.4789110E-03 5.0414085E-02 at 100iterations 6.2644313E-04 2.3811340E-02 at 110iterations 2.6648722E-04 9.4656944E-03 at 120iterations finished qdiffx linear iterations at : 08:07:01 total time elapsed so far: 9.140000 # loops : 120 mean,max change (kT/e) : 2.6648722E-04 9.4656944E-03 energy calculations done at 9.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 08:07:02 9.323u 0.294s 0:10.03 95.8% 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 08:07:02 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 = 3037 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.487616 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): 9.515000 72.47100 ymin,ymax (A): -0.9660000 63.43300 zmin,zma (A): -4.963000 41.90500 x,y,z range (A): 62.95600 64.39900 46.86800 scale (grids/A): 2.487616 object centre (A): 40.99300 31.23350 18.47100 number of atom coordinates read : 3037 total number of charged atoms : 2890 net assigned charge : 8.500035 assigned positive charge : 451.7968 centred at (gu) : 91.66979 94.07077 80.96404 assigned negative charge : -443.2980 centred at (gu) : 92.53145 94.25328 80.45834 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 158750 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31066 grid for indexing accessible points = 1.400000 m= 69223 mr = 106872 m= 19549 mr = 52617 m= 3034 mr = 14087 m= 184 mr = 1788 m= 6 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.8600001 no. cavity mid-points inaccessible to solvent = 1396 time to turn everything in is 1.470000 number of dielectric boundary points 75307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 23096 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) : 1.658411 object centre at (A) : 40.99300 31.23350 18.47100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1612701 8.1938617E-02 midg,1,midg; midg,igrid,midg -4.1627530E-02 -0.1326640 1,midg,midg; igrid,midg,midg 0.3285805 -7.2555500E-03 gauss-seidel spectral radius is 0.9991686 estimated iterations to convergence 274 setup time was (sec) 1.790000 now iterating at: 08:07:04 rms-change max change #iterations 8.921593 308.6765 at 10iterations 5.110371 138.1894 at 20iterations 2.900403 70.38577 at 30iterations 1.636938 35.03400 at 40iterations 0.9194766 19.37193 at 50iterations 0.5159052 10.87803 at 60iterations 0.2881055 6.073084 at 70iterations 0.1608481 3.547952 at 80iterations 8.9587070E-02 1.660324 at 90iterations 4.9907919E-02 0.9638367 at 100iterations 2.7749885E-02 0.5414457 at 110iterations 1.5393378E-02 0.3228340 at 120iterations 8.5815629E-03 0.1729820 at 130iterations 4.7561992E-03 9.9899769E-02 at 140iterations 2.6384706E-03 5.3601742E-02 at 150iterations 1.4618865E-03 3.1045914E-02 at 160iterations 8.1253005E-04 1.6405106E-02 at 170iterations 4.5141217E-04 9.3078613E-03 at 180iterations finished qdiffx linear iterations at : 08:07:18 total time elapsed so far: 15.40000 # loops : 180 mean,max change (kT/e) : 4.5141217E-04 9.3078613E-03 energy calculations done at 15.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.59000 DelPhi exited at 08:07:18 15.589u 0.303s 0:16.50 96.2% 0+0k 0+0io 0pf+0w