Tue Oct 11 03:57:30 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 Tue Oct 11 2011 at 03:57:30 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6328551 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): -11.98600 37.02700 ymin,ymax (A): -25.92900 22.28800 zmin,zma (A): -10.53600 45.71700 x,y,z range (A): 49.01300 48.21700 56.25300 scale (grids/A): 0.6328551 object centre (A): 12.52050 -1.820499 17.59050 number of atom coordinates read : 2756 total number of charged atoms : 2604 net assigned charge : 1.162012 assigned positive charge : 414.4158 centred at (gu) : 90.27897 90.36501 91.75698 assigned negative charge : -413.2544 centred at (gu) : 90.07953 90.24693 91.70008 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7265 nv = 96 ne = 84 npr = 56539 no. pairs analyzed = 56539 no. exposed pairs = 3331 no. arc points = 23127 no. surface atoms = 1115 nbur = 1641 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 4050 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3700000 number of dielectric boundary points 3548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2382 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8897 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1491594E-09 1.0204995E-08 midg,1,midg; midg,igrid,midg -1.0138818E-08 1.4118270E-08 1,midg,midg; igrid,midg,midg -1.8394442E-08 2.2352937E-08 gauss-seidel spectral radius is 0.9870755 estimated iterations to convergence 72 setup time was (sec) 0.6400000 now iterating at: 03:57:31 rms-change max change #iterations 0.1426556 19.01309 at 10iterations 1.4021460E-02 1.979462 at 20iterations 1.4479745E-03 0.1904449 at 30iterations 1.6625260E-04 2.3300171E-02 at 40iterations 2.8112181E-05 4.3821335E-03 at 50iterations finished qdiffx linear iterations at : 03:57:34 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 2.8112181E-05 4.3821335E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 03:57:34 4.086u 0.267s 0:04.72 91.9% 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 03:57:34 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.898565 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): -11.98600 37.02700 ymin,ymax (A): -25.92900 22.28800 zmin,zma (A): -10.53600 45.71700 x,y,z range (A): 49.01300 48.21700 56.25300 scale (grids/A): 1.898565 object centre (A): 12.52050 -1.820499 17.59050 number of atom coordinates read : 2756 total number of charged atoms : 2604 net assigned charge : 1.162012 assigned positive charge : 414.4158 centred at (gu) : 90.83642 91.09480 95.27024 assigned negative charge : -413.2544 centred at (gu) : 90.23856 90.74064 95.10001 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 78806 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23127 grid for indexing accessible points = 1.400000 m= 28059 mr = 55458 m= 3942 mr = 20584 m= 207 mr = 2325 m= 5 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 562 time to turn everything in is 0.6900000 number of dielectric boundary points 32600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 20478 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) : 0.6328551 object centre at (A) : 12.52050 -1.820499 17.59050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4328395E-02 3.6490377E-04 midg,1,midg; midg,igrid,midg -1.0651333E-02 1.9337254E-02 1,midg,midg; igrid,midg,midg -5.6401095E-03 5.0252821E-02 gauss-seidel spectral radius is 0.9986403 estimated iterations to convergence 215 setup time was (sec) 0.9800000 now iterating at: 03:57:36 rms-change max change #iterations 4.342784 208.0700 at 10iterations 2.036845 66.71900 at 20iterations 0.9584510 30.96954 at 30iterations 0.4502493 14.94160 at 40iterations 0.2114482 7.539709 at 50iterations 9.9597268E-02 3.338285 at 60iterations 4.6764754E-02 1.469294 at 70iterations 2.1992810E-02 0.6824012 at 80iterations 1.0345629E-02 0.3027477 at 90iterations 4.8552440E-03 0.1613197 at 100iterations 2.2890191E-03 7.0922852E-02 at 110iterations 1.0767446E-03 3.1897068E-02 at 120iterations finished qdiffx linear iterations at : 03:57:44 total time elapsed so far: 9.280000 # loops : 120 mean,max change (kT/e) : 1.0767446E-03 3.1897068E-02 energy calculations done at 9.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.460000 DelPhi exited at 03:57:45 9.466u 0.305s 0:10.11 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 Tue Oct 11 2011 at 03:57:45 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.847848 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): -11.98600 37.02700 ymin,ymax (A): -25.92900 22.28800 zmin,zma (A): -10.53600 45.71700 x,y,z range (A): 49.01300 48.21700 56.25300 scale (grids/A): 2.847848 object centre (A): 12.52050 -1.820499 17.59050 number of atom coordinates read : 2756 total number of charged atoms : 2604 net assigned charge : 1.162012 assigned positive charge : 414.4158 centred at (gu) : 91.25437 91.64201 97.90527 assigned negative charge : -413.2544 centred at (gu) : 90.35767 91.11087 97.64989 start vw surface at 0.1700000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 182209 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23127 grid for indexing accessible points = 1.400000 m= 91959 mr = 134239 m= 31687 mr = 75418 m= 7098 mr = 25160 m= 871 mr = 5110 m= 38 mr = 530 m= 0 mr = 7 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 1921 time to turn everything in is 1.790000 number of dielectric boundary points 73398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 20827 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) : 1.898565 object centre at (A) : 12.52050 -1.820499 17.59050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7241304 0.2474362 midg,1,midg; midg,igrid,midg -0.1442428 0.2645847 1,midg,midg; igrid,midg,midg -4.3496203E-02 0.4640843 gauss-seidel spectral radius is 0.9992597 estimated iterations to convergence 290 setup time was (sec) 2.110000 now iterating at: 03:57:47 rms-change max change #iterations 10.22832 357.4441 at 10iterations 5.979008 146.2742 at 20iterations 3.486369 73.02766 at 30iterations 2.021922 42.40036 at 40iterations 1.174131 24.48615 at 50iterations 0.6780437 12.56602 at 60iterations 0.3912781 7.975079 at 70iterations 0.2262188 3.993800 at 80iterations 0.1306773 2.409316 at 90iterations 7.5481042E-02 1.447762 at 100iterations 4.3387037E-02 0.7978096 at 110iterations 2.5017679E-02 0.5447998 at 120iterations 1.4439170E-02 0.2624464 at 130iterations 8.3371857E-03 0.1420593 at 140iterations 4.8122578E-03 8.8127136E-02 at 150iterations 2.7951221E-03 5.0231934E-02 at 160iterations 1.6292683E-03 3.4378052E-02 at 170iterations 9.5789362E-04 1.8972874E-02 at 180iterations finished qdiffx linear iterations at : 03:58:01 total time elapsed so far: 15.76000 # loops : 180 mean,max change (kT/e) : 9.5789362E-04 1.8972874E-02 energy calculations done at 15.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.94000 DelPhi exited at 03:58:01 15.941u 0.304s 0:16.66 97.4% 0+0k 0+0io 0pf+0w