Sun Oct 9 02:43:36 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 Sun Oct 9 2011 at 02:43:36 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2172 !!! WARNING: SEP 119 has a net charge of -0.4750 !!! WARNING: GLM 120 has a net charge of -0.0940 !!! WARNING: HIT 142 has a net charge of 0.5140 !!! WARNING: MG3 319 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6870598 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): 0.5979999 41.47400 ymin,ymax (A): -24.43300 18.05200 zmin,zma (A): -32.82100 18.99400 x,y,z range (A): 40.87600 42.48500 51.81500 scale (grids/A): 0.6870598 object centre (A): 21.03600 -3.190500 -6.913500 number of atom coordinates read : 2172 total number of charged atoms : 2034 net assigned charge : -3.154987 assigned positive charge : 327.7086 centred at (gu) : 89.66728 90.23087 90.31565 assigned negative charge : -330.8639 centred at (gu) : 89.68507 90.21262 90.30813 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6897 nv = 96 ne = 84 npr = 46316 no. pairs analyzed = 46316 no. exposed pairs = 2407 no. arc points = 16796 no. surface atoms = 821 nbur = 1351 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 4155 m= 0 mr = 102 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 304 time to turn everything in is 0.1700000 number of dielectric boundary points 3070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1579 ## 131 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7775 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7621938E-08 -1.4653741E-08 midg,1,midg; midg,igrid,midg -2.1287041E-08 -1.0730479E-08 1,midg,midg; igrid,midg,midg -1.1101942E-08 -2.0720561E-08 gauss-seidel spectral radius is 0.9889701 estimated iterations to convergence 78 setup time was (sec) 0.3500000 now iterating at: 02:43:37 rms-change max change #iterations 0.1898202 28.19558 at 10iterations 2.2236871E-02 3.032742 at 20iterations 2.5530267E-03 0.3979492 at 30iterations 3.0004521E-04 4.1717529E-02 at 40iterations 3.4557419E-05 5.7129860E-03 at 50iterations finished qdiffx linear iterations at : 02:43:40 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 3.4557419E-05 5.7129860E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 02:43:40 3.308u 0.180s 0:03.78 92.0% 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 Sun Oct 9 2011 at 02:43:40 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2172 !!! WARNING: SEP 119 has a net charge of -0.4750 !!! WARNING: GLM 120 has a net charge of -0.0940 !!! WARNING: HIT 142 has a net charge of 0.5140 !!! WARNING: MG3 319 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.061179 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): 0.5979999 41.47400 ymin,ymax (A): -24.43300 18.05200 zmin,zma (A): -32.82100 18.99400 x,y,z range (A): 40.87600 42.48500 51.81500 scale (grids/A): 2.061179 object centre (A): 21.03600 -3.190500 -6.913500 number of atom coordinates read : 2172 total number of charged atoms : 2034 net assigned charge : -3.154987 assigned positive charge : 327.7086 centred at (gu) : 89.00161 90.69251 90.94650 assigned negative charge : -330.8639 centred at (gu) : 89.05522 90.63766 90.92437 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16796 grid for indexing accessible points = 1.400000 m= 29128 mr = 53295 m= 5639 mr = 22849 m= 504 mr = 4194 m= 7 mr = 325 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 8075 time to turn everything in is 0.3600000 number of dielectric boundary points 28199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 16125 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) : 0.6870598 object centre at (A) : 21.03600 -3.190500 -6.913500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8100588E-04 -1.4851002E-04 midg,1,midg; midg,igrid,midg 8.7607896E-04 -1.3109519E-02 1,midg,midg; igrid,midg,midg -9.0369666E-03 -1.3396430E-02 gauss-seidel spectral radius is 0.9987701 estimated iterations to convergence 226 setup time was (sec) 0.5600000 now iterating at: 02:43:41 rms-change max change #iterations 4.529375 181.9456 at 10iterations 2.205480 78.72924 at 20iterations 1.073662 34.96608 at 30iterations 0.5250750 16.36208 at 40iterations 0.2554419 8.204910 at 50iterations 0.1252053 4.437214 at 60iterations 6.0724448E-02 1.842397 at 70iterations 2.9618558E-02 0.9188395 at 80iterations 1.4378640E-02 0.4723015 at 90iterations 7.0109335E-03 0.2012291 at 100iterations 3.4286047E-03 0.1117620 at 110iterations 1.6702735E-03 5.3227425E-02 at 120iterations finished qdiffx linear iterations at : 02:43:48 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 1.6702735E-03 5.3227425E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 02:43:48 7.658u 0.199s 0:08.12 96.5% 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 Sun Oct 9 2011 at 02:43:48 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2172 !!! WARNING: SEP 119 has a net charge of -0.4750 !!! WARNING: GLM 120 has a net charge of -0.0940 !!! WARNING: HIT 142 has a net charge of 0.5140 !!! WARNING: MG3 319 has a net charge of 1.4000 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: 3.091769 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): 0.5979999 41.47400 ymin,ymax (A): -24.43300 18.05200 zmin,zma (A): -32.82100 18.99400 x,y,z range (A): 40.87600 42.48500 51.81500 scale (grids/A): 3.091769 object centre (A): 21.03600 -3.190500 -6.913500 number of atom coordinates read : 2172 total number of charged atoms : 2034 net assigned charge : -3.154987 assigned positive charge : 327.7086 centred at (gu) : 88.50230 91.03874 91.41979 assigned negative charge : -330.8639 centred at (gu) : 88.58277 90.95662 91.38667 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 169915 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16796 grid for indexing accessible points = 1.400000 m= 91014 mr = 127861 m= 37194 mr = 77150 m= 10842 mr = 31768 m= 2270 mr = 9057 m= 287 mr = 1923 m= 7 mr = 208 m= 0 mr = 3 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 27598 time to turn everything in is 1.080000 number of dielectric boundary points 63559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 16272 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) : 2.061179 object centre at (A) : 21.03600 -3.190500 -6.913500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5885106E-02 0.1415531 midg,1,midg; midg,igrid,midg 9.7151205E-02 -0.1842713 1,midg,midg; igrid,midg,midg -3.6659259E-02 -0.1982201 gauss-seidel spectral radius is 0.9992727 estimated iterations to convergence 293 setup time was (sec) 1.310000 now iterating at: 02:43:50 rms-change max change #iterations 10.07378 398.0998 at 10iterations 5.809848 107.7060 at 20iterations 3.347813 65.08195 at 30iterations 1.929729 33.76765 at 40iterations 1.111303 23.49721 at 50iterations 0.6410160 11.16217 at 60iterations 0.3692268 6.436356 at 70iterations 0.2132199 3.582924 at 80iterations 0.1230302 2.193451 at 90iterations 7.0804283E-02 1.268826 at 100iterations 4.0837832E-02 0.7165450 at 110iterations 2.3481872E-02 0.4108505 at 120iterations 1.3558856E-02 0.2345686 at 130iterations 7.8296615E-03 0.1357408 at 140iterations 4.5177913E-03 8.1634521E-02 at 150iterations 2.6074937E-03 4.8046112E-02 at 160iterations 1.5034318E-03 2.5602877E-02 at 170iterations 8.6745503E-04 1.5239716E-02 at 180iterations finished qdiffx linear iterations at : 02:44:01 total time elapsed so far: 12.36000 # loops : 180 mean,max change (kT/e) : 8.6745503E-04 1.5239716E-02 energy calculations done at 12.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.50000 DelPhi exited at 02:44:01 12.502u 0.198s 0:13.05 97.2% 0+0k 0+0io 0pf+0w