Sat Oct 8 22:21:10 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 Sat Oct 8 2011 at 22:21:10 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2337 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: 0.6420199 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): -27.27400 26.27500 ymin,ymax (A): 8.467000 52.48900 zmin,zma (A): -11.84900 43.60100 x,y,z range (A): 53.54900 44.02200 55.45000 scale (grids/A): 0.6420199 object centre (A): -0.4995003 30.47800 15.87600 number of atom coordinates read : 2337 total number of charged atoms : 2202 net assigned charge : 9.000025 assigned positive charge : 340.1695 centred at (gu) : 90.88605 90.80372 90.97377 assigned negative charge : -331.1701 centred at (gu) : 90.87166 90.66593 90.97340 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6719 nv = 96 ne = 84 npr = 46597 no. pairs analyzed = 46597 no. exposed pairs = 3156 no. arc points = 22788 no. surface atoms = 1054 nbur = 1283 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 3452 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.1800000 number of dielectric boundary points 3589 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2188 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7801 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1207378E-08 1.6825446E-08 midg,1,midg; midg,igrid,midg -6.9814327E-10 3.3178136E-08 1,midg,midg; igrid,midg,midg 1.0191816E-08 1.8306004E-08 gauss-seidel spectral radius is 0.9874180 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 22:21:11 rms-change max change #iterations 0.1359755 21.13702 at 10iterations 1.3437286E-02 1.798786 at 20iterations 1.3312766E-03 0.2108383 at 30iterations 1.3304815E-04 1.8970490E-02 at 40iterations 1.3725812E-05 2.1553040E-03 at 50iterations finished qdiffx linear iterations at : 22:21:14 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.3725812E-05 2.1553040E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 22:21:14 3.537u 0.205s 0:04.00 93.2% 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 Sat Oct 8 2011 at 22:21:14 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2337 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: 1.926060 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): -27.27400 26.27500 ymin,ymax (A): 8.467000 52.48900 zmin,zma (A): -11.84900 43.60100 x,y,z range (A): 53.54900 44.02200 55.45000 scale (grids/A): 1.926060 object centre (A): -0.4995003 30.47800 15.87600 number of atom coordinates read : 2337 total number of charged atoms : 2202 net assigned charge : 9.000025 assigned positive charge : 340.1695 centred at (gu) : 92.65797 92.41073 92.92104 assigned negative charge : -331.1701 centred at (gu) : 92.61513 91.99792 92.92043 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 71003 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22788 grid for indexing accessible points = 1.400000 m= 25206 mr = 46985 m= 3907 mr = 17730 m= 228 mr = 2349 m= 4 mr = 82 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 248 time to turn everything in is 0.3500000 number of dielectric boundary points 33200 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17369 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) : 0.6420199 object centre at (A) : -0.4995003 30.47800 15.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5524314E-02 3.4607213E-02 midg,1,midg; midg,igrid,midg -1.1331374E-02 2.7286235E-02 1,midg,midg; igrid,midg,midg 3.6258280E-02 5.0499268E-02 gauss-seidel spectral radius is 0.9986511 estimated iterations to convergence 216 setup time was (sec) 0.5800000 now iterating at: 22:21:15 rms-change max change #iterations 3.998777 192.5997 at 10iterations 1.880919 72.58382 at 20iterations 0.8855022 30.80365 at 30iterations 0.4142506 15.20258 at 40iterations 0.1947392 6.383472 at 50iterations 9.1012448E-02 3.018230 at 60iterations 4.2952288E-02 1.461329 at 70iterations 2.0163225E-02 0.6392362 at 80iterations 9.4735622E-03 0.3127623 at 90iterations 4.4452427E-03 0.1454811 at 100iterations 2.0920364E-03 6.7731857E-02 at 110iterations 9.8252937E-04 3.1402588E-02 at 120iterations finished qdiffx linear iterations at : 22:21:22 total time elapsed so far: 8.080000 # loops : 120 mean,max change (kT/e) : 9.8252937E-04 3.1402588E-02 energy calculations done at 8.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.210000 DelPhi exited at 22:21:23 8.213u 0.238s 0:08.73 96.6% 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 Sat Oct 8 2011 at 22:21:23 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2337 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: 2.889089 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): -27.27400 26.27500 ymin,ymax (A): 8.467000 52.48900 zmin,zma (A): -11.84900 43.60100 x,y,z range (A): 53.54900 44.02200 55.45000 scale (grids/A): 2.889089 object centre (A): -0.4995003 30.47800 15.87600 number of atom coordinates read : 2337 total number of charged atoms : 2202 net assigned charge : 9.000025 assigned positive charge : 340.1695 centred at (gu) : 93.98672 93.61600 94.38151 assigned negative charge : -331.1701 centred at (gu) : 93.92265 92.99696 94.38061 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 164078 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22788 grid for indexing accessible points = 1.400000 m= 80694 mr = 114475 m= 29165 mr = 64200 m= 6965 mr = 22799 m= 973 mr = 5054 m= 68 mr = 672 m= 2 mr = 36 m= 0 mr = 2 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 792 time to turn everything in is 0.9500000 number of dielectric boundary points 74707 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 17612 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) : 1.926060 object centre at (A) : -0.4995003 30.47800 15.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7379687 0.4013945 midg,1,midg; midg,igrid,midg -0.1131960 0.2438662 1,midg,midg; igrid,midg,midg 0.3737752 0.4532891 gauss-seidel spectral radius is 0.9992734 estimated iterations to convergence 293 setup time was (sec) 1.190000 now iterating at: 22:21:24 rms-change max change #iterations 9.523913 457.2753 at 10iterations 5.634962 153.3042 at 20iterations 3.300019 72.32254 at 30iterations 1.928700 45.76634 at 40iterations 1.124688 24.37848 at 50iterations 0.6548706 15.33761 at 60iterations 0.3789370 8.193823 at 70iterations 0.2197245 4.358293 at 80iterations 0.1272687 2.724930 at 90iterations 7.3747024E-02 1.308435 at 100iterations 4.2599287E-02 0.7773585 at 110iterations 2.4615005E-02 0.4420400 at 120iterations 1.4270057E-02 0.2674174 at 130iterations 8.2274927E-03 0.1548977 at 140iterations 4.7581070E-03 8.8775635E-02 at 150iterations 2.7457310E-03 5.1514626E-02 at 160iterations 1.5843842E-03 2.9684067E-02 at 170iterations 9.1430935E-04 1.6759396E-02 at 180iterations finished qdiffx linear iterations at : 22:21:36 total time elapsed so far: 13.33000 # loops : 180 mean,max change (kT/e) : 9.1430935E-04 1.6759396E-02 energy calculations done at 13.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.46000 DelPhi exited at 22:21:37 13.465u 0.238s 0:13.96 98.0% 0+0k 0+0io 0pf+0w