Mon Oct 10 14:01:22 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 Mon Oct 10 2011 at 14:01:22 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4656 !!! WARNING: GLM 204 has a net charge of -0.0940 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: 0.5405651 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): 21.39600 78.77600 ymin,ymax (A): 118.9750 184.8320 zmin,zma (A): -1.841000 59.94200 x,y,z range (A): 57.38000 65.85700 61.78300 scale (grids/A): 0.5405651 object centre (A): 50.08600 151.9035 29.05050 number of atom coordinates read : 4656 total number of charged atoms : 4483 net assigned charge : 2.906039 assigned positive charge : 709.6981 centred at (gu) : 90.82867 89.26128 87.35796 assigned negative charge : -706.7957 centred at (gu) : 90.84795 89.18434 87.40945 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8672 nv = 96 ne = 84 npr = 94041 no. pairs analyzed = 94041 no. exposed pairs = 5727 no. arc points = 39420 no. surface atoms = 1917 nbur = 2739 mkacc time = 0.2700000 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 = 1.568000 m= 386 mr = 4636 m= 0 mr = 24 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4031 ## 550 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 11665 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1278636E-09 -1.5413650E-10 midg,1,midg; midg,igrid,midg -6.3341160E-10 6.5479960E-10 1,midg,midg; igrid,midg,midg 2.4659449E-10 -3.3775194E-11 gauss-seidel spectral radius is 0.9824820 estimated iterations to convergence 62 setup time was (sec) 0.8000000 now iterating at: 14:01:23 rms-change max change #iterations 8.9251548E-02 16.74523 at 10iterations 7.0666787E-03 1.102425 at 20iterations 2.0600206E-03 0.3626709 at 30iterations 1.0096204E-03 0.1781769 at 40iterations 5.0442183E-04 8.8489532E-02 at 50iterations finished qdiffx linear iterations at : 14:01:26 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 5.0442183E-04 8.8489532E-02 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 14:01:27 4.283u 0.276s 0:05.23 86.9% 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 Mon Oct 10 2011 at 14:01:27 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4656 !!! WARNING: GLM 204 has a net charge of -0.0940 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: 1.621695 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): 21.39600 78.77600 ymin,ymax (A): 118.9750 184.8320 zmin,zma (A): -1.841000 59.94200 x,y,z range (A): 57.38000 65.85700 61.78300 scale (grids/A): 1.621695 object centre (A): 50.08600 151.9035 29.05050 number of atom coordinates read : 4656 total number of charged atoms : 4483 net assigned charge : 2.906039 assigned positive charge : 709.6981 centred at (gu) : 92.48473 87.78267 82.07274 assigned negative charge : -706.7957 centred at (gu) : 92.54360 87.55286 82.22817 start vw surface at 0.2200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 98456 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39420 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 30746 mr = 69250 m= 3296 mr = 20866 m= 98 mr = 1626 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 40842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 465 ## 5 charges are in solution ## iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 34204 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) : 0.5405651 object centre at (A) : 50.08600 151.9035 29.05050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3696940E-03 9.4660996E-03 midg,1,midg; midg,igrid,midg 1.2829808E-02 2.8813409E-02 1,midg,midg; igrid,midg,midg -1.6692577E-02 -1.4749561E-02 gauss-seidel spectral radius is 0.9983207 estimated iterations to convergence 194 setup time was (sec) 1.170000 now iterating at: 14:01:29 rms-change max change #iterations 4.308059 178.3381 at 10iterations 1.852710 62.61763 at 20iterations 0.7962132 26.96804 at 30iterations 0.3447625 10.71041 at 40iterations 0.1488486 4.657097 at 50iterations 6.4628333E-02 1.937515 at 60iterations 2.8384561E-02 0.8700619 at 70iterations 1.2832339E-02 0.3715096 at 80iterations 6.2969425E-03 0.2109623 at 90iterations 3.5791283E-03 0.1339340 at 100iterations 2.3956548E-03 8.2649231E-02 at 110iterations 1.7725509E-03 5.9375763E-02 at 120iterations finished qdiffx linear iterations at : 14:01:37 total time elapsed so far: 9.640000 # loops : 120 mean,max change (kT/e) : 1.7725509E-03 5.9375763E-02 energy calculations done at 9.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.820000 DelPhi exited at 14:01:38 9.820u 0.299s 0:10.47 96.5% 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 14:01:38 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4656 !!! WARNING: GLM 204 has a net charge of -0.0940 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: 2.432543 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): 21.39600 78.77600 ymin,ymax (A): 118.9750 184.8320 zmin,zma (A): -1.841000 59.94200 x,y,z range (A): 57.38000 65.85700 61.78300 scale (grids/A): 2.432543 object centre (A): 50.08600 151.9035 29.05050 number of atom coordinates read : 4656 total number of charged atoms : 4483 net assigned charge : 2.906039 assigned positive charge : 709.6981 centred at (gu) : 93.72682 86.67378 78.10887 assigned negative charge : -706.7957 centred at (gu) : 93.81531 86.32916 78.34228 start vw surface at 0.2200000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 229157 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39420 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 107311 mr = 169382 m= 30469 mr = 84772 m= 5300 mr = 22650 m= 404 mr = 3503 m= 9 mr = 185 m= 0 mr = 2 time to grow re-entrant surface = 1.320000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.140000 number of dielectric boundary points 92156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 35817 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) : 1.621695 object centre at (A) : 50.08600 151.9035 29.05050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3135115E-03 0.2191118 midg,1,midg; midg,igrid,midg 0.1913023 0.4930514 1,midg,midg; igrid,midg,midg -0.2842571 -0.2011025 gauss-seidel spectral radius is 0.9992133 estimated iterations to convergence 281 setup time was (sec) 2.480000 now iterating at: 14:01:41 rms-change max change #iterations 11.08020 274.8853 at 10iterations 6.446347 142.6920 at 20iterations 3.717967 75.89844 at 30iterations 2.134026 38.91460 at 40iterations 1.224184 24.02068 at 50iterations 0.6988258 11.99745 at 60iterations 0.3977713 8.121958 at 70iterations 0.2261721 3.985418 at 80iterations 0.1286607 2.357050 at 90iterations 7.3121853E-02 1.232639 at 100iterations 4.1621584E-02 0.7446632 at 110iterations 2.3785641E-02 0.4572773 at 120iterations 1.3706176E-02 0.2528076 at 130iterations 8.0608679E-03 0.1560011 at 140iterations 4.9186307E-03 9.9849701E-02 at 150iterations 3.2096365E-03 7.2425842E-02 at 160iterations 2.2770488E-03 5.0495148E-02 at 170iterations 1.7465083E-03 3.8066864E-02 at 180iterations finished qdiffx linear iterations at : 14:01:55 total time elapsed so far: 16.74000 # loops : 180 mean,max change (kT/e) : 1.7465083E-03 3.8066864E-02 energy calculations done at 16.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.91000 DelPhi exited at 14:01:58 16.907u 0.321s 0:19.82 86.8% 0+0k 0+0io 0pf+0w