Sat Oct 8 12:33:52 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 Sat Oct 8 2011 at 12:33:52 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 = 2354 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: 0.6064116 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): -59.82000 -10.29000 ymin,ymax (A): -15.98600 42.72000 zmin,zma (A): -14.58800 26.96300 x,y,z range (A): 49.53000 58.70600 41.55100 scale (grids/A): 0.6064116 object centre (A): -35.05500 13.36700 6.187500 number of atom coordinates read : 2354 total number of charged atoms : 2219 net assigned charge : -0.9999830 assigned positive charge : 319.1546 centred at (gu) : 91.37031 90.89117 90.36078 assigned negative charge : -320.1552 centred at (gu) : 91.25093 90.58519 90.34847 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5814 nv = 96 ne = 84 npr = 50491 no. pairs analyzed = 50491 no. exposed pairs = 3056 no. arc points = 21424 no. surface atoms = 1042 nbur = 1312 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 277 mr = 2895 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2800000 number of dielectric boundary points 3179 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2063 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7131 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0473297E-09 -2.5278588E-10 midg,1,midg; midg,igrid,midg -1.0022513E-08 1.2433382E-08 1,midg,midg; igrid,midg,midg -3.7491699E-09 4.9828199E-09 gauss-seidel spectral radius is 0.9859114 estimated iterations to convergence 69 setup time was (sec) 0.6000000 now iterating at: 12:33:53 rms-change max change #iterations 9.7878456E-02 17.14026 at 10iterations 9.5419697E-03 2.007214 at 20iterations 1.5460122E-03 0.3307533 at 30iterations 4.9630849E-04 0.1035347 at 40iterations 1.7491916E-04 3.6605835E-02 at 50iterations finished qdiffx linear iterations at : 12:33:57 total time elapsed so far: 4.980000 # loops : 50 mean,max change (kT/e) : 1.7491916E-04 3.6605835E-02 energy calculations done at 4.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.150000 DelPhi exited at 12:33:58 5.153u 0.465s 0:05.95 94.2% 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 Sat Oct 8 2011 at 12:33:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2354 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: 1.819235 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): -59.82000 -10.29000 ymin,ymax (A): -15.98600 42.72000 zmin,zma (A): -14.58800 26.96300 x,y,z range (A): 49.53000 58.70600 41.55100 scale (grids/A): 1.819235 object centre (A): -35.05500 13.36700 6.187500 number of atom coordinates read : 2354 total number of charged atoms : 2219 net assigned charge : -0.9999830 assigned positive charge : 319.1546 centred at (gu) : 94.11066 92.67343 91.08214 assigned negative charge : -320.1552 centred at (gu) : 93.75276 91.75582 91.04564 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 62760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21424 grid for indexing accessible points = 1.400000 m= 19885 mr = 41266 m= 2787 mr = 13208 m= 142 mr = 1551 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 426 time to turn everything in is 0.5400000 number of dielectric boundary points 29513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17352 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) : 0.6064116 object centre at (A) : -35.05500 13.36700 6.187500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7538470E-03 2.5624894E-03 midg,1,midg; midg,igrid,midg -3.1748492E-02 4.8502300E-02 1,midg,midg; igrid,midg,midg -3.9850734E-03 -1.6218167E-03 gauss-seidel spectral radius is 0.9984866 estimated iterations to convergence 204 setup time was (sec) 0.9000000 now iterating at: 12:33:59 rms-change max change #iterations 3.478433 164.0622 at 10iterations 1.549315 57.50545 at 20iterations 0.6954607 25.17698 at 30iterations 0.3131763 11.59805 at 40iterations 0.1407246 5.088985 at 50iterations 6.3666739E-02 2.222108 at 60iterations 2.8625458E-02 0.9907951 at 70iterations 1.3100188E-02 0.4264221 at 80iterations 6.0640085E-03 0.2531452 at 90iterations 2.9471347E-03 0.1182556 at 100iterations 1.5370842E-03 6.4250946E-02 at 110iterations 8.8702905E-04 3.9688110E-02 at 120iterations finished qdiffx linear iterations at : 12:34:10 total time elapsed so far: 12.06000 # loops : 120 mean,max change (kT/e) : 8.8702905E-04 3.9688110E-02 energy calculations done at 12.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.24000 DelPhi exited at 12:34:11 12.244u 0.513s 0:13.06 97.6% 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 12:34:11 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 = 2354 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.728852 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): -59.82000 -10.29000 ymin,ymax (A): -15.98600 42.72000 zmin,zma (A): -14.58800 26.96300 x,y,z range (A): 49.53000 58.70600 41.55100 scale (grids/A): 2.728852 object centre (A): -35.05500 13.36700 6.187500 number of atom coordinates read : 2354 total number of charged atoms : 2219 net assigned charge : -0.9999830 assigned positive charge : 319.1546 centred at (gu) : 96.16585 94.01012 91.62310 assigned negative charge : -320.1552 centred at (gu) : 95.62926 92.63371 91.56841 start vw surface at 0.1200000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 145621 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21424 grid for indexing accessible points = 1.400000 m= 65221 mr = 101075 m= 21630 mr = 50488 m= 4838 mr = 16131 m= 548 mr = 3425 m= 32 mr = 312 m= 0 mr = 15 time to grow re-entrant surface = 0.8000001 no. cavity mid-points inaccessible to solvent = 1477 time to turn everything in is 1.380000 number of dielectric boundary points 66444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 17750 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) : 1.819235 object centre at (A) : -35.05500 13.36700 6.187500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0106632E-02 1.7863695E-02 midg,1,midg; midg,igrid,midg -0.3987475 0.6021772 1,midg,midg; igrid,midg,midg -2.8317442E-02 -3.7595395E-02 gauss-seidel spectral radius is 0.9992151 estimated iterations to convergence 282 setup time was (sec) 1.780000 now iterating at: 12:34:13 rms-change max change #iterations 8.318474 276.5179 at 10iterations 4.755744 112.8353 at 20iterations 2.699873 73.65835 at 30iterations 1.530995 32.46076 at 40iterations 0.8646963 17.72285 at 50iterations 0.4902075 9.896067 at 60iterations 0.2771931 5.273116 at 70iterations 0.1567657 3.222847 at 80iterations 8.8498391E-02 1.781157 at 90iterations 5.0065253E-02 0.9729042 at 100iterations 2.8273717E-02 0.5949326 at 110iterations 1.5975526E-02 0.3412018 at 120iterations 9.0572061E-03 0.1884470 at 130iterations 5.1545962E-03 0.1033239 at 140iterations 2.9521384E-03 6.5488815E-02 at 150iterations 1.7153907E-03 4.2461395E-02 at 160iterations 1.0314295E-03 2.2823334E-02 at 170iterations 6.4875145E-04 1.6071320E-02 at 180iterations finished qdiffx linear iterations at : 12:34:33 total time elapsed so far: 21.46000 # loops : 180 mean,max change (kT/e) : 6.4875145E-04 1.6071320E-02 energy calculations done at 21.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.62000 DelPhi exited at 12:34:33 21.625u 0.561s 0:22.46 98.7% 0+0k 0+0io 0pf+0w