Tue Oct 11 08:22:34 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 08:22:34 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2792 !!! WARNING: SER 51 has a net charge of 0.5000 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: SEP 227 has a net charge of -0.4750 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6451262 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): -10.95900 37.41700 ymin,ymax (A): -26.99900 21.48800 zmin,zma (A): -9.696000 45.48700 x,y,z range (A): 48.37600 48.48700 55.18300 scale (grids/A): 0.6451262 object centre (A): 13.22900 -2.755501 17.89550 number of atom coordinates read : 2792 total number of charged atoms : 2637 net assigned charge : 3.201018 assigned positive charge : 424.0178 centred at (gu) : 89.74199 90.44741 91.59457 assigned negative charge : -420.8173 centred at (gu) : 89.51083 90.27386 91.57731 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7642 nv = 96 ne = 84 npr = 57424 no. pairs analyzed = 57424 no. exposed pairs = 3326 no. arc points = 22884 no. surface atoms = 1123 nbur = 1669 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 387 mr = 4373 m= 3 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2262 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9272 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1065525E-09 1.1011174E-08 midg,1,midg; midg,igrid,midg -1.8357539E-08 3.3085033E-08 1,midg,midg; igrid,midg,midg -3.0665198E-08 3.5992457E-08 gauss-seidel spectral radius is 0.9875615 estimated iterations to convergence 73 setup time was (sec) 0.5900000 now iterating at: 08:22:35 rms-change max change #iterations 0.1596834 22.49876 at 10iterations 1.6329922E-02 2.392944 at 20iterations 1.7852391E-03 0.2535348 at 30iterations 2.5127656E-04 3.8239479E-02 at 40iterations 5.7592828E-05 7.8988075E-03 at 50iterations finished qdiffx linear iterations at : 08:22:38 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 5.7592828E-05 7.8988075E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 08:22:39 3.432u 0.168s 0:04.26 84.2% 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 Tue Oct 11 2011 at 08:22:39 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2792 !!! WARNING: SER 51 has a net charge of 0.5000 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: SEP 227 has a net charge of -0.4750 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.935379 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): -10.95900 37.41700 ymin,ymax (A): -26.99900 21.48800 zmin,zma (A): -9.696000 45.48700 x,y,z range (A): 48.37600 48.48700 55.18300 scale (grids/A): 1.935379 object centre (A): 13.22900 -2.755501 17.89550 number of atom coordinates read : 2792 total number of charged atoms : 2637 net assigned charge : 3.201018 assigned positive charge : 424.0178 centred at (gu) : 89.22559 91.34177 94.78317 assigned negative charge : -420.8173 centred at (gu) : 88.53185 90.82119 94.73164 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 82593 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22884 grid for indexing accessible points = 1.400000 m= 31037 mr = 58609 m= 4900 mr = 23491 m= 273 mr = 3078 m= 1 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1005 time to turn everything in is 0.6200000 number of dielectric boundary points 33540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20811 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) : 0.6451262 object centre at (A) : 13.22900 -2.755501 17.89550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1847460E-02 8.5500777E-03 midg,1,midg; midg,igrid,midg -1.2583279E-02 2.2245860E-02 1,midg,midg; igrid,midg,midg -1.6188765E-02 5.7183638E-02 gauss-seidel spectral radius is 0.9986919 estimated iterations to convergence 219 setup time was (sec) 0.9100000 now iterating at: 08:22:40 rms-change max change #iterations 4.593145 235.9995 at 10iterations 2.187471 67.33633 at 20iterations 1.045147 33.44678 at 30iterations 0.4977028 15.27875 at 40iterations 0.2370368 6.762575 at 50iterations 0.1131218 3.496162 at 60iterations 5.4149292E-02 1.729973 at 70iterations 2.5712520E-02 0.7512714 at 80iterations 1.2276514E-02 0.3734913 at 90iterations 5.8449274E-03 0.1891599 at 100iterations 2.8038172E-03 8.0580652E-02 at 110iterations 1.3389476E-03 4.7090054E-02 at 120iterations finished qdiffx linear iterations at : 08:22:46 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 1.3389476E-03 4.7090054E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 08:22:47 7.892u 0.160s 0:08.55 94.1% 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 08:22:47 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2792 !!! WARNING: SER 51 has a net charge of 0.5000 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: SEP 227 has a net charge of -0.4750 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.903068 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): -10.95900 37.41700 ymin,ymax (A): -26.99900 21.48800 zmin,zma (A): -9.696000 45.48700 x,y,z range (A): 48.37600 48.48700 55.18300 scale (grids/A): 2.903068 object centre (A): 13.22900 -2.755501 17.89550 number of atom coordinates read : 2792 total number of charged atoms : 2637 net assigned charge : 3.201018 assigned positive charge : 424.0178 centred at (gu) : 88.83838 92.01257 97.17465 assigned negative charge : -420.8173 centred at (gu) : 87.79776 91.23180 97.09760 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 190901 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22884 grid for indexing accessible points = 1.400000 m= 99963 mr = 141461 m= 36548 mr = 83196 m= 8814 mr = 29797 m= 1268 mr = 6704 m= 70 mr = 830 m= 5 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 3466 time to turn everything in is 1.550000 number of dielectric boundary points 75542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 21096 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) : 1.935379 object centre at (A) : 13.22900 -2.755501 17.89550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3950202 0.3095607 midg,1,midg; midg,igrid,midg -0.1477586 0.2184250 1,midg,midg; igrid,midg,midg -0.1730978 0.5173582 gauss-seidel spectral radius is 0.9992707 estimated iterations to convergence 292 setup time was (sec) 1.870000 now iterating at: 08:22:49 rms-change max change #iterations 10.63794 418.9465 at 10iterations 6.235900 154.0770 at 20iterations 3.638181 79.23097 at 30iterations 2.119907 40.29511 at 40iterations 1.235616 25.43239 at 50iterations 0.7173551 14.23653 at 60iterations 0.4159377 7.943260 at 70iterations 0.2406148 4.336858 at 80iterations 0.1394805 2.399113 at 90iterations 8.0919370E-02 1.444684 at 100iterations 4.6816222E-02 0.8558383 at 110iterations 2.7152522E-02 0.4596891 at 120iterations 1.5678387E-02 0.2935181 at 130iterations 9.1006244E-03 0.1669693 at 140iterations 5.2772439E-03 9.4413757E-02 at 150iterations 3.0749273E-03 5.6690216E-02 at 160iterations 1.7946064E-03 3.4540176E-02 at 170iterations 1.0552572E-03 1.8398285E-02 at 180iterations finished qdiffx linear iterations at : 08:23:00 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 1.0552572E-03 1.8398285E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 08:23:01 12.944u 0.198s 0:13.45 97.6% 0+0k 0+0io 0pf+0w