Wed Dec 28 11:01:49 PST 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 Wed Dec 28 2011 at 11:01:49 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 0.6489601 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): -6.208000 34.52000 ymin,ymax (A): -3.531000 48.00500 zmin,zma (A): -23.98100 30.87600 x,y,z range (A): 40.72800 51.53600 54.85700 scale (grids/A): 0.6489601 object centre (A): 14.15600 22.23700 3.447500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 90.94126 92.58688 90.12172 assigned negative charge : -284.4403 centred at (gu) : 91.05946 92.74593 90.05760 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5579 nv = 96 ne = 84 npr = 40609 no. pairs analyzed = 40609 no. exposed pairs = 2416 no. arc points = 16981 no. surface atoms = 820 nbur = 1146 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 292 mr = 3137 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.2500000 number of dielectric boundary points 2693 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1665 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6579 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6708164E-11 1.4121984E-08 midg,1,midg; midg,igrid,midg 1.3831281E-08 -1.8906270E-08 1,midg,midg; igrid,midg,midg 1.5977541E-08 -7.4315256E-09 gauss-seidel spectral radius is 0.9876371 estimated iterations to convergence 73 setup time was (sec) 0.5300000 now iterating at: 11:01:50 rms-change max change #iterations 0.1307254 21.85384 at 10iterations 1.3335410E-02 2.481445 at 20iterations 1.3452147E-03 0.2158253 at 30iterations 1.3794709E-04 1.9691467E-02 at 40iterations 1.4174779E-05 2.0217896E-03 at 50iterations finished qdiffx linear iterations at : 11:01:56 total time elapsed so far: 6.920000 # loops : 50 mean,max change (kT/e) : 1.4174779E-05 2.0217896E-03 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 11:01:57 7.103u 0.506s 0:08.27 91.8% 0+0k 0+0io 6pf+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 Wed Dec 28 2011 at 11:01:57 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 1.946880 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): -6.208000 34.52000 ymin,ymax (A): -3.531000 48.00500 zmin,zma (A): -23.98100 30.87600 x,y,z range (A): 40.72800 51.53600 54.85700 scale (grids/A): 1.946880 object centre (A): 14.15600 22.23700 3.447500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 92.82393 97.76044 90.36536 assigned negative charge : -284.4403 centred at (gu) : 93.17854 98.23788 90.17316 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 60282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16981 grid for indexing accessible points = 1.400000 m= 21981 mr = 41913 m= 3476 mr = 16775 m= 198 mr = 2307 m= 3 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2029 time to turn everything in is 0.5500000 number of dielectric boundary points 24851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 94 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 14459 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) : 0.6489601 object centre at (A) : 14.15600 22.23700 3.447500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9798070E-02 1.7651876E-02 midg,1,midg; midg,igrid,midg 3.8373206E-02 -1.3116169E-02 1,midg,midg; igrid,midg,midg 1.1137299E-02 -3.8099319E-03 gauss-seidel spectral radius is 0.9986118 estimated iterations to convergence 213 setup time was (sec) 0.8900000 now iterating at: 11:01:59 rms-change max change #iterations 3.702825 185.8218 at 10iterations 1.727921 62.08232 at 20iterations 0.8082999 30.10079 at 30iterations 0.3755195 13.26382 at 40iterations 0.1740231 6.600433 at 50iterations 8.1110030E-02 2.728569 at 60iterations 3.7655350E-02 1.242491 at 70iterations 1.7607994E-02 0.6332340 at 80iterations 8.1601180E-03 0.2708921 at 90iterations 3.8057109E-03 0.1228757 at 100iterations 1.7656940E-03 5.8792114E-02 at 110iterations 8.2379946E-04 2.7640343E-02 at 120iterations finished qdiffx linear iterations at : 11:02:16 total time elapsed so far: 17.64000 # loops : 120 mean,max change (kT/e) : 8.2379946E-04 2.7640343E-02 energy calculations done at 17.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.80000 DelPhi exited at 11:02:17 17.802u 0.768s 0:20.52 90.4% 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 Wed Dec 28 2011 at 11:02:18 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 2.920320 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): -6.208000 34.52000 ymin,ymax (A): -3.531000 48.00500 zmin,zma (A): -23.98100 30.87600 x,y,z range (A): 40.72800 51.53600 54.85700 scale (grids/A): 2.920320 object centre (A): 14.15600 22.23700 3.447500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 94.23592 101.6406 90.54784 assigned negative charge : -284.4403 centred at (gu) : 94.76794 102.3568 90.25977 start vw surface at 0.1100000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 139535 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16981 grid for indexing accessible points = 1.400000 m= 70987 mr = 101342 m= 26098 mr = 59170 m= 6234 mr = 21643 m= 970 mr = 4923 m= 62 mr = 662 m= 0 mr = 33 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 6208 time to turn everything in is 1.300000 number of dielectric boundary points 56113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 14655 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) : 1.946880 object centre at (A) : 14.15600 22.23700 3.447500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8929247 5.6195933E-02 midg,1,midg; midg,igrid,midg 0.3701494 -0.1597142 1,midg,midg; igrid,midg,midg 7.9886973E-02 -7.2659487E-03 gauss-seidel spectral radius is 0.9992386 estimated iterations to convergence 286 setup time was (sec) 1.700000 now iterating at: 11:02:20 rms-change max change #iterations 8.629431 465.7307 at 10iterations 4.949116 108.6469 at 20iterations 2.805562 53.78286 at 30iterations 1.597100 33.27107 at 40iterations 0.9085264 22.37984 at 50iterations 0.5177129 12.10806 at 60iterations 0.2943776 5.936449 at 70iterations 0.1669450 3.235476 at 80iterations 9.5032491E-02 1.902735 at 90iterations 5.4091275E-02 1.073128 at 100iterations 3.0700516E-02 0.6118164 at 110iterations 1.7449081E-02 0.3617799 at 120iterations 9.9413171E-03 0.1909599 at 130iterations 5.6343726E-03 0.1111410 at 140iterations 3.2129383E-03 6.7006588E-02 at 150iterations 1.8249491E-03 3.5515189E-02 at 160iterations 1.0406488E-03 2.0166039E-02 at 170iterations 5.9191609E-04 1.1955261E-02 at 180iterations finished qdiffx linear iterations at : 11:02:48 total time elapsed so far: 29.14000 # loops : 180 mean,max change (kT/e) : 5.9191609E-04 1.1955261E-02 energy calculations done at 29.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.32000 DelPhi exited at 11:02:48 29.321u 0.619s 0:30.64 97.6% 0+0k 0+0io 0pf+0w