Sat Oct 8 22:03:43 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 22:03:43 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 = 2307 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: 0.6487826 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): -30.89900 23.97300 ymin,ymax (A): 28.18900 70.62000 zmin,zma (A): -13.43200 40.80000 x,y,z range (A): 54.87200 42.43100 54.23200 scale (grids/A): 0.6487826 object centre (A): -3.463000 49.40450 13.68400 number of atom coordinates read : 2307 total number of charged atoms : 2172 net assigned charge : 10.50002 assigned positive charge : 335.6565 centred at (gu) : 91.68356 91.30968 89.67282 assigned negative charge : -325.1571 centred at (gu) : 91.65323 91.18530 89.69489 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6734 nv = 96 ne = 84 npr = 45661 no. pairs analyzed = 45661 no. exposed pairs = 3102 no. arc points = 22122 no. surface atoms = 1040 nbur = 1267 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 401 mr = 3503 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.1700000 number of dielectric boundary points 3575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2162 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7825 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3454426E-08 1.5439857E-08 midg,1,midg; midg,igrid,midg 3.0131726E-09 4.5241062E-08 1,midg,midg; igrid,midg,midg 1.1067349E-08 3.2544161E-08 gauss-seidel spectral radius is 0.9876738 estimated iterations to convergence 74 setup time was (sec) 0.3500000 now iterating at: 22:03:44 rms-change max change #iterations 0.1378528 22.62123 at 10iterations 1.4051510E-02 2.058678 at 20iterations 1.5153267E-03 0.2390118 at 30iterations 1.9508955E-04 3.2512665E-02 at 40iterations 3.4210829E-05 6.5135956E-03 at 50iterations finished qdiffx linear iterations at : 22:03:47 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 3.4210829E-05 6.5135956E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 22:03:47 3.310u 0.204s 0:03.90 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 Sat Oct 8 2011 at 22:03:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2307 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: 1.946348 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): -30.89900 23.97300 ymin,ymax (A): 28.18900 70.62000 zmin,zma (A): -13.43200 40.80000 x,y,z range (A): 54.87200 42.43100 54.23200 scale (grids/A): 1.946348 object centre (A): -3.463000 49.40450 13.68400 number of atom coordinates read : 2307 total number of charged atoms : 2172 net assigned charge : 10.50002 assigned positive charge : 335.6565 centred at (gu) : 95.05032 93.92867 89.01847 assigned negative charge : -325.1571 centred at (gu) : 94.95963 93.55611 89.08467 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22122 grid for indexing accessible points = 1.400000 m= 26393 mr = 47303 m= 4752 mr = 19226 m= 376 mr = 3058 m= 6 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1274 time to turn everything in is 0.3700000 number of dielectric boundary points 33141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 17112 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) : 0.6487826 object centre at (A) : -3.463000 49.40450 13.68400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1047841E-02 4.8752237E-02 midg,1,midg; midg,igrid,midg -9.9057937E-03 3.0417360E-02 1,midg,midg; igrid,midg,midg 4.1926000E-02 3.2494664E-02 gauss-seidel spectral radius is 0.9986734 estimated iterations to convergence 218 setup time was (sec) 0.5700000 now iterating at: 22:03:48 rms-change max change #iterations 4.010443 216.5048 at 10iterations 1.893568 72.95591 at 20iterations 0.8913612 43.81923 at 30iterations 0.4200753 13.83479 at 40iterations 0.1981964 5.732521 at 50iterations 9.4367549E-02 3.055179 at 60iterations 4.4476669E-02 1.470693 at 70iterations 2.1081749E-02 0.6873798 at 80iterations 9.9918526E-03 0.3118105 at 90iterations 4.7595846E-03 0.1497374 at 100iterations 2.2621294E-03 7.8037262E-02 at 110iterations 1.0814961E-03 3.7643433E-02 at 120iterations finished qdiffx linear iterations at : 22:03:55 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 1.0814961E-03 3.7643433E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 22:03:55 7.660u 0.213s 0:08.29 94.9% 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 22:03:56 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 = 2307 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: 2.919522 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): -30.89900 23.97300 ymin,ymax (A): 28.18900 70.62000 zmin,zma (A): -13.43200 40.80000 x,y,z range (A): 54.87200 42.43100 54.23200 scale (grids/A): 2.919522 object centre (A): -3.463000 49.40450 13.68400 number of atom coordinates read : 2307 total number of charged atoms : 2172 net assigned charge : 10.50002 assigned positive charge : 335.6565 centred at (gu) : 97.57540 95.89281 88.52754 assigned negative charge : -325.1571 centred at (gu) : 97.43938 95.33420 88.62700 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 164855 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22122 grid for indexing accessible points = 1.400000 m= 82805 mr = 115054 m= 32431 mr = 66726 m= 8729 mr = 26128 m= 1494 mr = 6637 m= 116 mr = 1047 m= 3 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 4111 time to turn everything in is 0.9400000 number of dielectric boundary points 74774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 17376 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) : 1.946348 object centre at (A) : -3.463000 49.40450 13.68400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5771108 0.4712946 midg,1,midg; midg,igrid,midg -0.1084673 0.2784623 1,midg,midg; igrid,midg,midg 0.5630324 0.3823205 gauss-seidel spectral radius is 0.9992773 estimated iterations to convergence 294 setup time was (sec) 1.170000 now iterating at: 22:03:57 rms-change max change #iterations 9.659250 434.2821 at 10iterations 5.752740 141.1674 at 20iterations 3.401239 84.22672 at 30iterations 1.999344 45.56799 at 40iterations 1.169804 23.35423 at 50iterations 0.6845199 15.54261 at 60iterations 0.3998122 7.897951 at 70iterations 0.2323837 4.746235 at 80iterations 0.1352330 3.120964 at 90iterations 7.8500882E-02 1.647903 at 100iterations 4.5554210E-02 0.8356457 at 110iterations 2.6415983E-02 0.4861155 at 120iterations 1.5312670E-02 0.2927551 at 130iterations 8.8919327E-03 0.1552620 at 140iterations 5.1507330E-03 0.1018634 at 150iterations 2.9909096E-03 5.8267117E-02 at 160iterations 1.7368192E-03 3.4187317E-02 at 170iterations 1.0156797E-03 1.8653870E-02 at 180iterations finished qdiffx linear iterations at : 22:04:08 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 1.0156797E-03 1.8653870E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 22:04:09 12.456u 0.306s 0:13.04 97.7% 0+0k 0+0io 0pf+0w