Tue Oct 11 06:02:46 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 Tue Oct 11 2011 at 06:02:46 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.7038077 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): 25.76500 72.20100 ymin,ymax (A): -18.96300 31.61900 zmin,zma (A): 4.000000 46.26600 x,y,z range (A): 46.43600 50.58200 42.26600 scale (grids/A): 0.7038077 object centre (A): 48.98300 6.328000 25.13300 number of atom coordinates read : 2327 total number of charged atoms : 1998 net assigned charge : 5.564011 assigned positive charge : 326.4259 centred at (gu) : 89.22264 90.23556 90.36041 assigned negative charge : -320.8621 centred at (gu) : 89.34864 90.17019 90.44838 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7192 nv = 96 ne = 84 npr = 42618 no. pairs analyzed = 42618 no. exposed pairs = 2585 no. arc points = 17600 no. surface atoms = 886 nbur = 1441 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 491 mr = 4176 m= 1 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1609 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7981 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7907615E-08 9.7159669E-10 midg,1,midg; midg,igrid,midg 1.1415376E-08 7.6539159E-08 1,midg,midg; igrid,midg,midg 1.1766587E-07 -1.4313921E-08 gauss-seidel spectral radius is 0.9894812 estimated iterations to convergence 79 setup time was (sec) 0.3600000 now iterating at: 06:02:46 rms-change max change #iterations 0.1998621 35.54020 at 10iterations 2.5637317E-02 3.619476 at 20iterations 3.7034231E-03 0.4650002 at 30iterations 7.7027187E-04 9.5800400E-02 at 40iterations 2.2651620E-04 2.5571823E-02 at 50iterations finished qdiffx linear iterations at : 06:02:49 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 2.2651620E-04 2.5571823E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 06:02:50 3.333u 0.166s 0:04.19 83.2% 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 06:02:50 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.111423 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): 25.76500 72.20100 ymin,ymax (A): -18.96300 31.61900 zmin,zma (A): 4.000000 46.26600 x,y,z range (A): 46.43600 50.58200 42.26600 scale (grids/A): 2.111423 object centre (A): 48.98300 6.328000 25.13300 number of atom coordinates read : 2327 total number of charged atoms : 1998 net assigned charge : 5.564011 assigned positive charge : 326.4259 centred at (gu) : 87.66790 90.70642 91.08126 assigned negative charge : -320.8621 centred at (gu) : 88.04599 90.51041 91.34515 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75904 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17600 grid for indexing accessible points = 1.400000 m= 31127 mr = 54236 m= 5959 mr = 23682 m= 541 mr = 3960 m= 19 mr = 256 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 31416 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15858 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) : 0.7038077 object centre at (A) : 48.98300 6.328000 25.13300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8719699E-02 2.3348372E-02 midg,1,midg; midg,igrid,midg 3.9335273E-02 2.6519831E-02 1,midg,midg; igrid,midg,midg 4.0305533E-02 -4.5684677E-02 gauss-seidel spectral radius is 0.9988247 estimated iterations to convergence 231 setup time was (sec) 0.6100000 now iterating at: 06:02:51 rms-change max change #iterations 4.639685 189.5619 at 10iterations 2.289062 76.33340 at 20iterations 1.132532 36.93316 at 30iterations 0.5625583 17.26050 at 40iterations 0.2787939 10.01286 at 50iterations 0.1384988 4.188166 at 60iterations 6.8713114E-02 2.191383 at 70iterations 3.4218322E-02 1.164033 at 80iterations 1.7242489E-02 0.5561447 at 90iterations 8.6898664E-03 0.2489823 at 100iterations 4.4440222E-03 0.1329041 at 110iterations 2.3741615E-03 7.1701050E-02 at 120iterations finished qdiffx linear iterations at : 06:02:58 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 2.3741615E-03 7.1701050E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 06:02:58 7.773u 0.193s 0:08.25 96.4% 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 Tue Oct 11 2011 at 06:02:58 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 3.167135 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): 25.76500 72.20100 ymin,ymax (A): -18.96300 31.61900 zmin,zma (A): 4.000000 46.26600 x,y,z range (A): 46.43600 50.58200 42.26600 scale (grids/A): 3.167135 object centre (A): 48.98300 6.328000 25.13300 number of atom coordinates read : 2327 total number of charged atoms : 1998 net assigned charge : 5.564011 assigned positive charge : 326.4259 centred at (gu) : 86.50181 91.05980 91.62193 assigned negative charge : -320.8621 centred at (gu) : 87.06895 90.76552 92.01777 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 174771 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17600 grid for indexing accessible points = 1.400000 m= 96422 mr = 130200 m= 39635 mr = 80442 m= 11193 mr = 32660 m= 2117 mr = 8664 m= 246 mr = 1512 m= 20 mr = 139 m= 0 mr = 8 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.170000 number of dielectric boundary points 70779 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 15984 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) : 2.111423 object centre at (A) : 48.98300 6.328000 25.13300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1081886 0.1996445 midg,1,midg; midg,igrid,midg 0.2934589 0.1156760 1,midg,midg; igrid,midg,midg 0.4125685 -0.5579220 gauss-seidel spectral radius is 0.9992962 estimated iterations to convergence 297 setup time was (sec) 1.410000 now iterating at: 06:03:00 rms-change max change #iterations 10.42885 346.7104 at 10iterations 6.174339 182.9694 at 20iterations 3.655648 75.43269 at 30iterations 2.153848 41.29525 at 40iterations 1.267636 25.28278 at 50iterations 0.7455191 14.21382 at 60iterations 0.4379166 7.798759 at 70iterations 0.2565200 4.776886 at 80iterations 0.1506616 2.600510 at 90iterations 8.8436306E-02 1.647204 at 100iterations 5.2055348E-02 1.043564 at 110iterations 3.0743528E-02 0.5360293 at 120iterations 1.8304637E-02 0.3176556 at 130iterations 1.1143101E-02 0.2114563 at 140iterations 6.9458298E-03 0.1540184 at 150iterations 4.5077316E-03 9.1499329E-02 at 160iterations 3.1045058E-03 6.4598083E-02 at 170iterations 2.2617935E-03 4.4342041E-02 at 180iterations finished qdiffx linear iterations at : 06:03:12 total time elapsed so far: 13.23000 # loops : 180 mean,max change (kT/e) : 2.2617935E-03 4.4342041E-02 energy calculations done at 13.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.35000 DelPhi exited at 06:03:13 13.356u 0.219s 0:14.12 96.0% 0+0k 0+0io 0pf+0w