Tue Oct 11 08:41:30 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 08:41:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 !!! WARNING: LEU 262 has a net charge of -0.2720 !!! WARNING: ILE 289 has a net charge of -0.2720 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: 0.6585641 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): -10.61300 37.09600 ymin,ymax (A): -27.04800 21.28800 zmin,zma (A): -8.677000 45.38000 x,y,z range (A): 47.70900 48.33600 54.05700 scale (grids/A): 0.6585641 object centre (A): 13.24150 -2.880000 18.35150 number of atom coordinates read : 2762 total number of charged atoms : 2613 net assigned charge : 3.956023 assigned positive charge : 417.5496 centred at (gu) : 89.93588 90.32238 91.28530 assigned negative charge : -413.5943 centred at (gu) : 89.68084 90.12630 91.24765 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7893 nv = 96 ne = 84 npr = 57126 no. pairs analyzed = 57126 no. exposed pairs = 3380 no. arc points = 23122 no. surface atoms = 1136 nbur = 1626 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 444 mr = 4437 m= 3 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.3100000 number of dielectric boundary points 3828 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2331 ## 230 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9516 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5498277E-09 2.2427249E-08 midg,1,midg; midg,igrid,midg -2.8986655E-08 5.1948994E-08 1,midg,midg; igrid,midg,midg -4.4245152E-08 5.9140003E-08 gauss-seidel spectral radius is 0.9880588 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 08:41:31 rms-change max change #iterations 0.1691307 22.99676 at 10iterations 1.7969375E-02 2.505101 at 20iterations 2.0681617E-03 0.2975559 at 30iterations 3.0256869E-04 4.1864395E-02 at 40iterations 7.1912124E-05 1.1093140E-02 at 50iterations finished qdiffx linear iterations at : 08:41:33 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 7.1912124E-05 1.1093140E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 08:41:34 3.334u 0.152s 0:03.91 89.0% 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 Tue Oct 11 2011 at 08:41:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 !!! WARNING: LEU 262 has a net charge of -0.2720 !!! WARNING: ILE 289 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.975692 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): -10.61300 37.09600 ymin,ymax (A): -27.04800 21.28800 zmin,zma (A): -8.677000 45.38000 x,y,z range (A): 47.70900 48.33600 54.05700 scale (grids/A): 1.975692 object centre (A): 13.24150 -2.880000 18.35150 number of atom coordinates read : 2762 total number of charged atoms : 2613 net assigned charge : 3.956023 assigned positive charge : 417.5496 centred at (gu) : 89.80697 90.96648 93.85547 assigned negative charge : -413.5943 centred at (gu) : 89.04197 90.37884 93.74232 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 84814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23122 grid for indexing accessible points = 1.400000 m= 32158 mr = 59862 m= 5438 mr = 23924 m= 394 mr = 3584 m= 1 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1131 time to turn everything in is 0.6400000 number of dielectric boundary points 35287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 20625 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) : 0.6585641 object centre at (A) : 13.24150 -2.880000 18.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0986462E-02 1.2127411E-02 midg,1,midg; midg,igrid,midg -1.7572928E-02 3.7367269E-02 1,midg,midg; igrid,midg,midg -1.3068711E-02 6.7332186E-02 gauss-seidel spectral radius is 0.9987409 estimated iterations to convergence 223 setup time was (sec) 0.9300000 now iterating at: 08:41:35 rms-change max change #iterations 4.716117 302.0812 at 10iterations 2.286476 68.68237 at 20iterations 1.103902 33.41791 at 30iterations 0.5325552 15.35312 at 40iterations 0.2579412 7.374979 at 50iterations 0.1248641 3.712548 at 60iterations 6.0241353E-02 1.760828 at 70iterations 2.9138571E-02 0.8417187 at 80iterations 1.4149302E-02 0.4105186 at 90iterations 6.8555102E-03 0.2037573 at 100iterations 3.3493659E-03 0.1053829 at 110iterations 1.6261442E-03 5.3745270E-02 at 120iterations finished qdiffx linear iterations at : 08:41:41 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 1.6261442E-03 5.3745270E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 08:41:42 7.580u 0.162s 0:08.11 95.4% 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 08:41:42 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 = 2762 !!! WARNING: LEU 262 has a net charge of -0.2720 !!! WARNING: ILE 289 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.963539 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): -10.61300 37.09600 ymin,ymax (A): -27.04800 21.28800 zmin,zma (A): -8.677000 45.38000 x,y,z range (A): 47.70900 48.33600 54.05700 scale (grids/A): 2.963539 object centre (A): 13.24150 -2.880000 18.35150 number of atom coordinates read : 2762 total number of charged atoms : 2613 net assigned charge : 3.956023 assigned positive charge : 417.5496 centred at (gu) : 89.71021 91.44968 95.78304 assigned negative charge : -413.5943 centred at (gu) : 88.56289 90.56816 95.61333 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 196260 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23122 grid for indexing accessible points = 1.400000 m= 102281 mr = 144979 m= 38987 mr = 84210 m= 9985 mr = 31731 m= 1585 mr = 7610 m= 122 mr = 1142 m= 2 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 3662 time to turn everything in is 1.610000 number of dielectric boundary points 79479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 20903 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) : 1.975692 object centre at (A) : 13.24150 -2.880000 18.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4966964 0.3426831 midg,1,midg; midg,igrid,midg -0.2072238 0.3961429 1,midg,midg; igrid,midg,midg -9.0706393E-02 0.6009891 gauss-seidel spectral radius is 0.9992857 estimated iterations to convergence 295 setup time was (sec) 1.910000 now iterating at: 08:41:44 rms-change max change #iterations 10.87994 413.0784 at 10iterations 6.415579 140.8581 at 20iterations 3.774770 92.96461 at 30iterations 2.213725 47.54495 at 40iterations 1.293906 24.34445 at 50iterations 0.7578869 18.34164 at 60iterations 0.4431257 7.866620 at 70iterations 0.2582046 4.424724 at 80iterations 0.1505872 2.484071 at 90iterations 8.7714396E-02 1.501015 at 100iterations 5.1262319E-02 0.8875427 at 110iterations 2.9931005E-02 0.5333881 at 120iterations 1.7492807E-02 0.2851558 at 130iterations 1.0241694E-02 0.1819019 at 140iterations 6.0349409E-03 0.1064949 at 150iterations 3.6018302E-03 6.8017960E-02 at 160iterations 2.1887091E-03 4.0771484E-02 at 170iterations 1.3628782E-03 2.5428772E-02 at 180iterations finished qdiffx linear iterations at : 08:41:54 total time elapsed so far: 11.99000 # loops : 180 mean,max change (kT/e) : 1.3628782E-03 2.5428772E-02 energy calculations done at 11.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 08:41:55 12.181u 0.189s 0:12.78 96.7% 0+0k 0+0io 0pf+0w