Mon Oct 10 14:08:04 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 Mon Oct 10 2011 at 14:08:04 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6477320 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): -52.26700 2.694000 ymin,ymax (A): -71.45500 -23.20000 zmin,zma (A): -32.02700 18.77500 x,y,z range (A): 54.96100 48.25500 50.80200 scale (grids/A): 0.6477320 object centre (A): -24.78650 -47.32750 -6.626000 number of atom coordinates read : 2371 total number of charged atoms : 2238 net assigned charge : -3.499990 assigned positive charge : 358.9432 centred at (gu) : 90.77403 91.06998 90.06162 assigned negative charge : -362.4438 centred at (gu) : 90.59862 90.98615 89.98227 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6713 nv = 96 ne = 84 npr = 48608 no. pairs analyzed = 48608 no. exposed pairs = 3031 no. arc points = 21290 no. surface atoms = 1028 nbur = 1343 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 428 mr = 3602 m= 4 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3487 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2008 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7888 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7152999E-08 3.9500763E-09 midg,1,midg; midg,igrid,midg -1.4360092E-08 5.7570468E-09 1,midg,midg; igrid,midg,midg -2.5965369E-08 1.9487171E-08 gauss-seidel spectral radius is 0.9876342 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 14:08:05 rms-change max change #iterations 0.1534350 21.68776 at 10iterations 1.5520187E-02 2.563663 at 20iterations 1.7932791E-03 0.2795353 at 30iterations 3.1563584E-04 4.9919128E-02 at 40iterations 8.2485938E-05 1.3231277E-02 at 50iterations finished qdiffx linear iterations at : 14:08:07 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 8.2485938E-05 1.3231277E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 14:08:08 3.579u 0.204s 0:04.46 84.5% 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 Mon Oct 10 2011 at 14:08:08 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 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: 1.943196 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): -52.26700 2.694000 ymin,ymax (A): -71.45500 -23.20000 zmin,zma (A): -32.02700 18.77500 x,y,z range (A): 54.96100 48.25500 50.80200 scale (grids/A): 1.943196 object centre (A): -24.78650 -47.32750 -6.626000 number of atom coordinates read : 2371 total number of charged atoms : 2238 net assigned charge : -3.499990 assigned positive charge : 358.9432 centred at (gu) : 92.32178 93.20950 90.18443 assigned negative charge : -362.4438 centred at (gu) : 91.79587 92.95834 89.94690 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 71582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21290 grid for indexing accessible points = 1.400000 m= 26915 mr = 48735 m= 4834 mr = 19671 m= 368 mr = 3009 m= 5 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 32182 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 17642 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) : 0.6477320 object centre at (A) : -24.78650 -47.32750 -6.626000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2562942E-02 -9.1380961E-03 midg,1,midg; midg,igrid,midg -1.9501342E-02 2.7918493E-04 1,midg,midg; igrid,midg,midg -9.7745452E-03 3.8597882E-02 gauss-seidel spectral radius is 0.9986725 estimated iterations to convergence 217 setup time was (sec) 0.9600000 now iterating at: 14:08:09 rms-change max change #iterations 4.290985 168.8733 at 10iterations 2.020181 80.50601 at 20iterations 0.9601663 33.82500 at 30iterations 0.4530913 14.57118 at 40iterations 0.2140633 6.648521 at 50iterations 0.1014996 3.182029 at 60iterations 4.8071302E-02 1.533867 at 70iterations 2.2845851E-02 0.7770796 at 80iterations 1.0834788E-02 0.3309183 at 90iterations 5.1627569E-03 0.1888847 at 100iterations 2.4917184E-03 7.6165974E-02 at 110iterations 1.2092855E-03 3.9405823E-02 at 120iterations finished qdiffx linear iterations at : 14:08:16 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 1.2092855E-03 3.9405823E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 14:08:17 8.043u 0.237s 0:08.58 96.3% 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 Mon Oct 10 2011 at 14:08:17 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 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: 2.914794 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): -52.26700 2.694000 ymin,ymax (A): -71.45500 -23.20000 zmin,zma (A): -32.02700 18.77500 x,y,z range (A): 54.96100 48.25500 50.80200 scale (grids/A): 2.914794 object centre (A): -24.78650 -47.32750 -6.626000 number of atom coordinates read : 2371 total number of charged atoms : 2238 net assigned charge : -3.499990 assigned positive charge : 358.9432 centred at (gu) : 93.48249 94.81413 90.27659 assigned negative charge : -362.4438 centred at (gu) : 92.69368 94.43758 89.92030 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 165304 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21290 grid for indexing accessible points = 1.400000 m= 84545 mr = 118349 m= 33059 mr = 68539 m= 8913 mr = 26435 m= 1403 mr = 6514 m= 111 mr = 884 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.470000 number of dielectric boundary points 72573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 17900 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) : 1.943196 object centre at (A) : -24.78650 -47.32750 -6.626000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1765298 -0.2837220 midg,1,midg; midg,igrid,midg -0.1098239 8.0854356E-02 1,midg,midg; igrid,midg,midg 6.6562362E-02 0.5508761 gauss-seidel spectral radius is 0.9992663 estimated iterations to convergence 291 setup time was (sec) 1.830000 now iterating at: 14:08:19 rms-change max change #iterations 9.961378 512.9545 at 10iterations 5.839024 134.3508 at 20iterations 3.401334 66.01707 at 30iterations 1.972721 36.56007 at 40iterations 1.146906 21.21373 at 50iterations 0.6648245 12.09224 at 60iterations 0.3834451 8.388724 at 70iterations 0.2214856 4.063516 at 80iterations 0.1277702 2.373795 at 90iterations 7.3531725E-02 1.421537 at 100iterations 4.2446956E-02 0.7977142 at 110iterations 2.4455518E-02 0.4444275 at 120iterations 1.4112819E-02 0.2594916 at 130iterations 8.1342952E-03 0.1565781 at 140iterations 4.6973885E-03 8.0455780E-02 at 150iterations 2.7098714E-03 4.7043800E-02 at 160iterations 1.5687150E-03 2.8921127E-02 at 170iterations 9.1108261E-04 1.7695427E-02 at 180iterations finished qdiffx linear iterations at : 14:08:31 total time elapsed so far: 13.54000 # loops : 180 mean,max change (kT/e) : 9.1108261E-04 1.7695427E-02 energy calculations done at 13.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.74000 DelPhi exited at 14:08:31 13.740u 0.250s 0:14.32 97.6% 0+0k 0+0io 0pf+0w