Tue Oct 11 04:17:35 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 04:17:35 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2789 !!! WARNING: HIR 43 has a net charge of 0.5140 !!! WARNING: ASP 291 has a net charge of -0.2720 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6569842 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): -8.512000 40.66700 ymin,ymax (A): -26.45400 22.08800 zmin,zma (A): -9.625999 44.56100 x,y,z range (A): 49.17900 48.54200 54.18700 scale (grids/A): 0.6569842 object centre (A): 16.07750 -2.183001 17.46750 number of atom coordinates read : 2789 total number of charged atoms : 2637 net assigned charge : 2.882024 assigned positive charge : 423.7675 centred at (gu) : 89.96920 90.37220 88.47301 assigned negative charge : -420.8863 centred at (gu) : 90.19831 90.21580 88.53778 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7971 nv = 96 ne = 84 npr = 57421 no. pairs analyzed = 57421 no. exposed pairs = 3461 no. arc points = 23770 no. surface atoms = 1167 nbur = 1622 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 464 mr = 4487 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3100000 number of dielectric boundary points 3897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2301 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9525 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6507479E-08 -4.5935624E-09 midg,1,midg; midg,igrid,midg -2.3120462E-08 3.9964338E-08 1,midg,midg; igrid,midg,midg 5.1099700E-08 -3.9806391E-08 gauss-seidel spectral radius is 0.9880054 estimated iterations to convergence 75 setup time was (sec) 0.5300000 now iterating at: 04:17:36 rms-change max change #iterations 0.1707417 21.70129 at 10iterations 1.8606668E-02 2.690651 at 20iterations 2.0261188E-03 0.2683792 at 30iterations 2.5800106E-04 4.2842865E-02 at 40iterations 4.7518606E-05 7.2708130E-03 at 50iterations finished qdiffx linear iterations at : 04:17:38 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 4.7518606E-05 7.2708130E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 04:17:39 3.154u 0.177s 0:04.03 82.3% 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 04:17:39 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2789 !!! WARNING: HIR 43 has a net charge of 0.5140 !!! WARNING: ASP 291 has a net charge of -0.2720 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.970953 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): -8.512000 40.66700 ymin,ymax (A): -26.45400 22.08800 zmin,zma (A): -9.625999 44.56100 x,y,z range (A): 49.17900 48.54200 54.18700 scale (grids/A): 1.970953 object centre (A): 16.07750 -2.183001 17.46750 number of atom coordinates read : 2789 total number of charged atoms : 2637 net assigned charge : 2.882024 assigned positive charge : 423.7675 centred at (gu) : 89.90676 91.11594 85.41842 assigned negative charge : -420.8863 centred at (gu) : 90.59457 90.64719 85.61295 start vw surface at 0.2200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 85842 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23770 grid for indexing accessible points = 1.400000 m= 31885 mr = 60474 m= 5356 mr = 23609 m= 348 mr = 3308 m= 2 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 479 time to turn everything in is 0.6900000 number of dielectric boundary points 35914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 20808 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) : 0.6569842 object centre at (A) : 16.07750 -2.183001 17.46750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3359365E-03 -6.2076926E-02 midg,1,midg; midg,igrid,midg -1.5032422E-02 3.2758959E-02 1,midg,midg; igrid,midg,midg 7.2749645E-02 -4.0245452E-03 gauss-seidel spectral radius is 0.9987391 estimated iterations to convergence 223 setup time was (sec) 0.9500000 now iterating at: 04:17:41 rms-change max change #iterations 4.790411 214.7154 at 10iterations 2.311962 75.73073 at 20iterations 1.116242 34.28845 at 30iterations 0.5404486 16.59100 at 40iterations 0.2607802 7.290388 at 50iterations 0.1262889 4.203445 at 60iterations 6.0847048E-02 1.833808 at 70iterations 2.9452335E-02 0.8495178 at 80iterations 1.4215071E-02 0.4083357 at 90iterations 6.8893577E-03 0.1976662 at 100iterations 3.3297867E-03 9.7990990E-02 at 110iterations 1.6165995E-03 4.6974182E-02 at 120iterations finished qdiffx linear iterations at : 04:17:46 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 1.6165995E-03 4.6974182E-02 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 04:17:47 7.056u 0.168s 0:07.75 93.0% 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 Tue Oct 11 2011 at 04:17:47 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2789 !!! WARNING: HIR 43 has a net charge of 0.5140 !!! WARNING: ASP 291 has a net charge of -0.2720 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.956429 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): -8.512000 40.66700 ymin,ymax (A): -26.45400 22.08800 zmin,zma (A): -9.625999 44.56100 x,y,z range (A): 49.17900 48.54200 54.18700 scale (grids/A): 2.956429 object centre (A): 16.07750 -2.183001 17.46750 number of atom coordinates read : 2789 total number of charged atoms : 2637 net assigned charge : 2.882024 assigned positive charge : 423.7675 centred at (gu) : 89.86010 91.67389 83.12732 assigned negative charge : -420.8863 centred at (gu) : 90.89188 90.97080 83.41932 start vw surface at 0.1700000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 198460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23770 grid for indexing accessible points = 1.400000 m= 102582 mr = 146364 m= 38056 mr = 84225 m= 9491 mr = 30661 m= 1446 mr = 7012 m= 94 mr = 926 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 1746 time to turn everything in is 1.520000 number of dielectric boundary points 80902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 21088 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) : 1.970953 object centre at (A) : 16.07750 -2.183001 17.46750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2701582 -0.9510909 midg,1,midg; midg,igrid,midg -0.1666503 0.3815039 1,midg,midg; igrid,midg,midg 0.6331838 -2.0635327E-02 gauss-seidel spectral radius is 0.9992853 estimated iterations to convergence 295 setup time was (sec) 1.790000 now iterating at: 04:17:49 rms-change max change #iterations 10.95246 369.2831 at 10iterations 6.437655 138.2699 at 20iterations 3.781605 79.23842 at 30iterations 2.212121 44.66414 at 40iterations 1.295322 23.63878 at 50iterations 0.7577946 14.66822 at 60iterations 0.4418922 8.034897 at 70iterations 0.2577159 4.529172 at 80iterations 0.1499631 2.562503 at 90iterations 8.7304406E-02 1.523476 at 100iterations 5.0992221E-02 0.9001465 at 110iterations 2.9668801E-02 0.5253487 at 120iterations 1.7299550E-02 0.2921600 at 130iterations 1.0070857E-02 0.1951828 at 140iterations 5.9198011E-03 0.1085510 at 150iterations 3.4880955E-03 5.9623718E-02 at 160iterations 2.0760798E-03 4.0283203E-02 at 170iterations 1.2550344E-03 2.5161743E-02 at 180iterations finished qdiffx linear iterations at : 04:17:59 total time elapsed so far: 11.12000 # loops : 180 mean,max change (kT/e) : 1.2550344E-03 2.5161743E-02 energy calculations done at 11.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.29000 DelPhi exited at 04:17:59 11.289u 0.188s 0:11.93 96.0% 0+0k 0+0io 0pf+0w