Tue Oct 11 08:24:41 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 Tue Oct 11 2011 at 08:24:42 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6615993 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): -11.01300 36.85500 ymin,ymax (A): -25.71000 22.64500 zmin,zma (A): -8.584000 45.22500 x,y,z range (A): 47.86800 48.35500 53.80900 scale (grids/A): 0.6615993 object centre (A): 12.92100 -1.532499 18.32050 number of atom coordinates read : 2733 total number of charged atoms : 2581 net assigned charge : 2.176010 assigned positive charge : 416.0469 centred at (gu) : 90.11734 90.14533 91.29070 assigned negative charge : -413.8714 centred at (gu) : 89.84589 89.99850 91.20793 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7938 nv = 96 ne = 84 npr = 56186 no. pairs analyzed = 56186 no. exposed pairs = 3305 no. arc points = 23360 no. surface atoms = 1112 nbur = 1621 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 4523 m= 2 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.3300000 number of dielectric boundary points 3819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2259 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9414 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.7169028E-09 3.0860267E-08 midg,1,midg; midg,igrid,midg -2.6411524E-08 3.8394585E-08 1,midg,midg; igrid,midg,midg -5.4471737E-08 6.5004983E-08 gauss-seidel spectral radius is 0.9881667 estimated iterations to convergence 75 setup time was (sec) 0.6200000 now iterating at: 08:24:43 rms-change max change #iterations 0.1757543 24.60813 at 10iterations 1.9330919E-02 2.968155 at 20iterations 2.1294092E-03 0.2858810 at 30iterations 2.5773412E-04 3.5766602E-02 at 40iterations 4.4799082E-05 5.1536560E-03 at 50iterations finished qdiffx linear iterations at : 08:24:46 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 4.4799082E-05 5.1536560E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 08:24:48 4.472u 0.383s 0:06.14 78.9% 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 08:24:48 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.984798 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): -11.01300 36.85500 ymin,ymax (A): -25.71000 22.64500 zmin,zma (A): -8.584000 45.22500 x,y,z range (A): 47.86800 48.35500 53.80900 scale (grids/A): 1.984798 object centre (A): 12.92100 -1.532499 18.32050 number of atom coordinates read : 2733 total number of charged atoms : 2581 net assigned charge : 2.176010 assigned positive charge : 416.0469 centred at (gu) : 90.35159 90.43587 93.87194 assigned negative charge : -413.8714 centred at (gu) : 89.53736 89.99483 93.62360 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 85459 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23360 grid for indexing accessible points = 1.400000 m= 31823 mr = 60607 m= 5287 mr = 23801 m= 352 mr = 3385 m= 9 mr = 145 m= 0 mr = 2 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 1062 time to turn everything in is 0.6900000 number of dielectric boundary points 34990 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 142 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 20366 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) : 0.6615993 object centre at (A) : 12.92100 -1.532499 18.32050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4951487E-02 -6.2507712E-03 midg,1,midg; midg,igrid,midg -1.5616328E-02 3.0698616E-02 1,midg,midg; igrid,midg,midg -1.5821304E-02 7.9076193E-02 gauss-seidel spectral radius is 0.9987488 estimated iterations to convergence 224 setup time was (sec) 0.9800000 now iterating at: 08:24:49 rms-change max change #iterations 4.812573 196.9504 at 10iterations 2.335162 79.20612 at 20iterations 1.132334 42.89308 at 30iterations 0.5487404 17.15488 at 40iterations 0.2661074 7.282349 at 50iterations 0.1288855 3.738262 at 60iterations 6.2524386E-02 2.091610 at 70iterations 3.0301493E-02 0.9912793 at 80iterations 1.4712191E-02 0.4305115 at 90iterations 7.1505224E-03 0.2370949 at 100iterations 3.4952185E-03 0.1075706 at 110iterations 1.7113055E-03 5.0820351E-02 at 120iterations finished qdiffx linear iterations at : 08:24:59 total time elapsed so far: 10.70000 # loops : 120 mean,max change (kT/e) : 1.7113055E-03 5.0820351E-02 energy calculations done at 10.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.86000 DelPhi exited at 08:25:00 10.869u 0.464s 0:12.07 93.7% 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 08:25:00 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.977197 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): -11.01300 36.85500 ymin,ymax (A): -25.71000 22.64500 zmin,zma (A): -8.584000 45.22500 x,y,z range (A): 47.86800 48.35500 53.80900 scale (grids/A): 2.977197 object centre (A): 12.92100 -1.532499 18.32050 number of atom coordinates read : 2733 total number of charged atoms : 2581 net assigned charge : 2.176010 assigned positive charge : 416.0469 centred at (gu) : 90.52723 90.65366 95.80772 assigned negative charge : -413.8714 centred at (gu) : 89.30610 89.99217 95.43544 start vw surface at 0.1200000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 197376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23360 grid for indexing accessible points = 1.400000 m= 102539 mr = 146193 m= 38130 mr = 84785 m= 9718 mr = 31059 m= 1497 mr = 7415 m= 106 mr = 968 m= 3 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 3459 time to turn everything in is 1.830000 number of dielectric boundary points 78885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 20640 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) : 1.984798 object centre at (A) : 12.92100 -1.532499 18.32050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.201810 6.6936739E-02 midg,1,midg; midg,igrid,midg -0.1572325 0.3702037 1,midg,midg; igrid,midg,midg -9.0735145E-02 0.6562753 gauss-seidel spectral radius is 0.9992844 estimated iterations to convergence 295 setup time was (sec) 2.170000 now iterating at: 08:25:02 rms-change max change #iterations 10.97275 418.8547 at 10iterations 6.441218 146.4126 at 20iterations 3.774970 80.73463 at 30iterations 2.209347 49.81905 at 40iterations 1.294926 25.10836 at 50iterations 0.7557939 13.23656 at 60iterations 0.4406309 8.218536 at 70iterations 0.2570419 4.759962 at 80iterations 0.1500086 2.670681 at 90iterations 8.7257273E-02 1.503138 at 100iterations 5.0850108E-02 0.8816547 at 110iterations 2.9669931E-02 0.5214825 at 120iterations 1.7321859E-02 0.3314676 at 130iterations 1.0148553E-02 0.1774988 at 140iterations 5.9825759E-03 0.1044922 at 150iterations 3.5509877E-03 5.9001923E-02 at 160iterations 2.1456575E-03 4.0598869E-02 at 170iterations 1.3252117E-03 2.5058746E-02 at 180iterations finished qdiffx linear iterations at : 08:25:19 total time elapsed so far: 18.65000 # loops : 180 mean,max change (kT/e) : 1.3252117E-03 2.5058746E-02 energy calculations done at 18.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.82000 DelPhi exited at 08:25:19 18.828u 0.495s 0:19.61 98.4% 0+0k 0+0io 0pf+0w