Mon Oct 10 14:39:02 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 14:39:02 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2782 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: 0.5910969 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): -85.35500 -25.12800 ymin,ymax (A): -12.42100 41.01600 zmin,zma (A): -18.12500 35.79300 x,y,z range (A): 60.22701 53.43700 53.91800 scale (grids/A): 0.5910969 object centre (A): -55.24150 14.29750 8.834000 number of atom coordinates read : 2782 total number of charged atoms : 2607 net assigned charge : 4.500012 assigned positive charge : 418.2546 centred at (gu) : 90.64162 89.25967 88.94826 assigned negative charge : -413.7554 centred at (gu) : 90.59480 89.24426 88.98893 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6352 nv = 96 ne = 84 npr = 56208 no. pairs analyzed = 56208 no. exposed pairs = 3645 no. arc points = 25687 no. surface atoms = 1212 nbur = 1570 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 278 mr = 3275 m= 0 mr = 6 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3349 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2552 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8009 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3120875E-09 1.8166736E-10 midg,1,midg; midg,igrid,midg 1.1290452E-09 1.5797706E-09 1,midg,midg; igrid,midg,midg 3.7053874E-11 3.2210921E-09 gauss-seidel spectral radius is 0.9852042 estimated iterations to convergence 67 setup time was (sec) 0.5900000 now iterating at: 14:39:03 rms-change max change #iterations 9.9369533E-02 16.19296 at 10iterations 8.2152821E-03 1.325064 at 20iterations 6.8389898E-04 0.1023979 at 30iterations 5.6873665E-05 8.2359314E-03 at 40iterations 6.0594448E-06 9.7656250E-04 at 50iterations finished qdiffx linear iterations at : 14:39:06 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 6.0594448E-06 9.7656250E-04 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 14:39:06 3.546u 0.164s 0:04.11 90.0% 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 Mon Oct 10 2011 at 14:39:06 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2782 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.773291 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): -85.35500 -25.12800 ymin,ymax (A): -12.42100 41.01600 zmin,zma (A): -18.12500 35.79300 x,y,z range (A): 60.22701 53.43700 53.91800 scale (grids/A): 1.773291 object centre (A): -55.24150 14.29750 8.834000 number of atom coordinates read : 2782 total number of charged atoms : 2607 net assigned charge : 4.500012 assigned positive charge : 418.2546 centred at (gu) : 91.92432 87.77836 86.84428 assigned negative charge : -413.7554 centred at (gu) : 91.78428 87.73234 86.96632 start vw surface at 0.2200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 69264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25687 grid for indexing accessible points = 1.400000 m= 22695 mr = 47021 m= 2908 mr = 15469 m= 138 mr = 1490 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 31014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 211 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20243 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) : 0.5910969 object centre at (A) : -55.24150 14.29750 8.834000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2568845E-02 -6.5759588E-05 midg,1,midg; midg,igrid,midg 4.1211308E-03 6.7619802E-03 1,midg,midg; igrid,midg,midg -4.0662507E-04 4.1428089E-04 gauss-seidel spectral radius is 0.9984444 estimated iterations to convergence 201 setup time was (sec) 0.9100000 now iterating at: 14:39:08 rms-change max change #iterations 3.807098 175.7773 at 10iterations 1.689363 61.68748 at 20iterations 0.7496690 25.74363 at 30iterations 0.3326557 11.06226 at 40iterations 0.1482328 4.987106 at 50iterations 6.6065438E-02 2.307367 at 60iterations 2.9317509E-02 0.9825022 at 70iterations 1.3070626E-02 0.4998894 at 80iterations 5.8094179E-03 0.2139177 at 90iterations 2.5963720E-03 9.2126846E-02 at 100iterations 1.1600667E-03 4.2171001E-02 at 110iterations 5.1917665E-04 1.8618584E-02 at 120iterations finished qdiffx linear iterations at : 14:39:15 total time elapsed so far: 8.440000 # loops : 120 mean,max change (kT/e) : 5.1917665E-04 1.8618584E-02 energy calculations done at 8.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.640000 DelPhi exited at 14:39:16 8.646u 0.203s 0:09.28 95.2% 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 14:39:16 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2782 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.659936 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): -85.35500 -25.12800 ymin,ymax (A): -12.42100 41.01600 zmin,zma (A): -18.12500 35.79300 x,y,z range (A): 60.22701 53.43700 53.91800 scale (grids/A): 2.659936 object centre (A): -55.24150 14.29750 8.834000 number of atom coordinates read : 2782 total number of charged atoms : 2607 net assigned charge : 4.500012 assigned positive charge : 418.2546 centred at (gu) : 92.88644 86.66740 85.26631 assigned negative charge : -413.7554 centred at (gu) : 92.67625 86.59847 85.44953 start vw surface at 0.2100000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 160426 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25687 grid for indexing accessible points = 1.400000 m= 75824 mr = 114592 m= 23859 mr = 59711 m= 4859 mr = 17834 m= 548 mr = 3183 m= 19 mr = 267 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.7500001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 69945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 20848 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) : 1.773291 object centre at (A) : -55.24150 14.29750 8.834000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1393186 -3.2015290E-02 midg,1,midg; midg,igrid,midg 0.1210460 8.5418515E-02 1,midg,midg; igrid,midg,midg 5.8580600E-02 -0.1743668 gauss-seidel spectral radius is 0.9992110 estimated iterations to convergence 281 setup time was (sec) 1.690000 now iterating at: 14:39:18 rms-change max change #iterations 9.385775 292.3017 at 10iterations 5.434781 127.1410 at 20iterations 3.131221 68.41811 at 30iterations 1.793025 40.62665 at 40iterations 1.025689 24.09676 at 50iterations 0.5849096 13.25502 at 60iterations 0.3315039 8.362548 at 70iterations 0.1885338 4.050774 at 80iterations 0.1072111 2.106815 at 90iterations 6.0619999E-02 1.358459 at 100iterations 3.4337588E-02 0.7877426 at 110iterations 1.9441739E-02 0.3893809 at 120iterations 1.1004168E-02 0.2172090 at 130iterations 6.2201535E-03 0.1323924 at 140iterations 3.5212408E-03 8.1353188E-02 at 150iterations 1.9867253E-03 3.6748886E-02 at 160iterations 1.1259976E-03 2.1516800E-02 at 170iterations 6.3916267E-04 1.3626099E-02 at 180iterations finished qdiffx linear iterations at : 14:39:29 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 6.3916267E-04 1.3626099E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 14:39:29 12.816u 0.215s 0:13.62 95.5% 0+0k 0+0io 0pf+0w