Sat Oct 8 22:40:37 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 Sat Oct 8 2011 at 22:40:37 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 = 2290 !!! WARNING: ARG 36 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6654330 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): -13.02300 40.47600 ymin,ymax (A): -21.46600 30.26800 zmin,zma (A): 2.140000 45.77300 x,y,z range (A): 53.49900 51.73400 43.63300 scale (grids/A): 0.6654330 object centre (A): 13.72650 4.401000 23.95650 number of atom coordinates read : 2290 total number of charged atoms : 2155 net assigned charge : 10.72802 assigned positive charge : 334.1994 centred at (gu) : 89.45953 88.47242 89.43887 assigned negative charge : -323.4721 centred at (gu) : 89.45354 88.49967 89.52948 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7122 nv = 96 ne = 84 npr = 45114 no. pairs analyzed = 45114 no. exposed pairs = 3135 no. arc points = 22347 no. surface atoms = 1032 nbur = 1258 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 424 mr = 3680 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 100 time to turn everything in is 0.1900000 number of dielectric boundary points 3830 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2137 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8076 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4072903E-08 1.2637123E-08 midg,1,midg; midg,igrid,midg 4.9613391E-08 1.9396321E-08 1,midg,midg; igrid,midg,midg 3.3575528E-08 2.9113417E-08 gauss-seidel spectral radius is 0.9882781 estimated iterations to convergence 75 setup time was (sec) 0.3900000 now iterating at: 22:40:38 rms-change max change #iterations 0.1565407 28.28370 at 10iterations 1.6619200E-02 2.211792 at 20iterations 1.8595490E-03 0.2774525 at 30iterations 3.0977331E-04 4.0033340E-02 at 40iterations 9.3665491E-05 1.3257504E-02 at 50iterations finished qdiffx linear iterations at : 22:40:41 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 9.3665491E-05 1.3257504E-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) 3.500000 DelPhi exited at 22:40:41 3.502u 0.164s 0:04.01 91.2% 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 Sat Oct 8 2011 at 22:40:41 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 = 2290 !!! WARNING: ARG 36 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.996299 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): -13.02300 40.47600 ymin,ymax (A): -21.46600 30.26800 zmin,zma (A): 2.140000 45.77300 x,y,z range (A): 53.49900 51.73400 43.63300 scale (grids/A): 1.996299 object centre (A): 13.72650 4.401000 23.95650 number of atom coordinates read : 2290 total number of charged atoms : 2155 net assigned charge : 10.72802 assigned positive charge : 334.1994 centred at (gu) : 88.37827 85.41683 88.31647 assigned negative charge : -323.4721 centred at (gu) : 88.36065 85.49905 88.58840 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 75146 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22347 grid for indexing accessible points = 1.400000 m= 28497 mr = 50209 m= 5447 mr = 20474 m= 448 mr = 3386 m= 14 mr = 158 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2230 time to turn everything in is 0.3800000 number of dielectric boundary points 35326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 17024 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) : 0.6654330 object centre at (A) : 13.72650 4.401000 23.95650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9551307E-02 -1.2428265E-03 midg,1,midg; midg,igrid,midg 3.2206103E-02 5.5689745E-02 1,midg,midg; igrid,midg,midg 6.3413523E-02 4.4531990E-02 gauss-seidel spectral radius is 0.9987368 estimated iterations to convergence 223 setup time was (sec) 0.6100000 now iterating at: 22:40:42 rms-change max change #iterations 4.216334 205.0445 at 10iterations 2.035183 73.91699 at 20iterations 0.9746547 31.33415 at 30iterations 0.4695496 17.82037 at 40iterations 0.2257021 7.771988 at 50iterations 0.1087559 3.695917 at 60iterations 5.2639045E-02 1.731259 at 70iterations 2.5362348E-02 0.7811894 at 80iterations 1.2231216E-02 0.4020586 at 90iterations 5.9240744E-03 0.1968613 at 100iterations 2.8765621E-03 9.0904236E-02 at 110iterations 1.4333301E-03 4.4616699E-02 at 120iterations finished qdiffx linear iterations at : 22:40:49 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 1.4333301E-03 4.4616699E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 22:40:50 8.106u 0.222s 0:08.67 95.9% 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 Sat Oct 8 2011 at 22:40:50 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 = 2290 !!! WARNING: ARG 36 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.994448 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): -13.02300 40.47600 ymin,ymax (A): -21.46600 30.26800 zmin,zma (A): 2.140000 45.77300 x,y,z range (A): 53.49900 51.73400 43.63300 scale (grids/A): 2.994448 object centre (A): 13.72650 4.401000 23.95650 number of atom coordinates read : 2290 total number of charged atoms : 2155 net assigned charge : 10.72802 assigned positive charge : 334.1994 centred at (gu) : 87.56736 83.12518 87.47454 assigned negative charge : -323.4721 centred at (gu) : 87.54103 83.24861 87.88270 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 173412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22347 grid for indexing accessible points = 1.400000 m= 89101 mr = 122064 m= 35322 mr = 71488 m= 9913 mr = 27975 m= 1800 mr = 7268 m= 164 mr = 1224 m= 4 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 7615 time to turn everything in is 1.020000 number of dielectric boundary points 79643 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 17236 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) : 1.996299 object centre at (A) : 13.72650 4.401000 23.95650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2369221 -3.4423798E-02 midg,1,midg; midg,igrid,midg 0.3621928 0.6726993 1,midg,midg; igrid,midg,midg 0.5537046 0.4048163 gauss-seidel spectral radius is 0.9992919 estimated iterations to convergence 297 setup time was (sec) 1.270000 now iterating at: 22:40:51 rms-change max change #iterations 9.915298 396.2859 at 10iterations 5.916617 142.4918 at 20iterations 3.520674 72.09561 at 30iterations 2.080872 44.59495 at 40iterations 1.228941 25.44836 at 50iterations 0.7221272 14.26155 at 60iterations 0.4241371 8.326998 at 70iterations 0.2485658 5.030787 at 80iterations 0.1456795 2.900393 at 90iterations 8.5321710E-02 1.582092 at 100iterations 4.9914360E-02 0.9566402 at 110iterations 2.9120570E-02 0.5324345 at 120iterations 1.7007764E-02 0.3126874 at 130iterations 9.9323345E-03 0.2185173 at 140iterations 5.8039008E-03 0.1044731 at 150iterations 3.3847622E-03 6.5816879E-02 at 160iterations 1.9819746E-03 3.4212589E-02 at 170iterations 1.1667156E-03 2.1984100E-02 at 180iterations finished qdiffx linear iterations at : 22:41:04 total time elapsed so far: 13.64000 # loops : 180 mean,max change (kT/e) : 1.1667156E-03 2.1984100E-02 energy calculations done at 13.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.77000 DelPhi exited at 22:41:04 13.774u 0.229s 0:14.35 97.4% 0+0k 0+0io 0pf+0w