Sat Oct 8 23:32:08 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 23:32:08 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 = 2390 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6348867 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): 80.70200 122.8590 ymin,ymax (A): 65.73300 121.8060 zmin,zma (A): 54.93100 108.3570 x,y,z range (A): 42.15701 56.07300 53.42600 scale (grids/A): 0.6348867 object centre (A): 101.7805 93.76950 81.64400 number of atom coordinates read : 2390 total number of charged atoms : 2255 net assigned charge : 11.50002 assigned positive charge : 347.7543 centred at (gu) : 91.05177 89.32584 89.45582 assigned negative charge : -336.2551 centred at (gu) : 90.96723 89.35664 89.44306 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6649 nv = 96 ne = 84 npr = 47872 no. pairs analyzed = 47872 no. exposed pairs = 3059 no. arc points = 21998 no. surface atoms = 1029 nbur = 1361 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 416 mr = 3520 m= 3 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3506 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2182 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7855 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4775170E-08 1.3781393E-08 midg,1,midg; midg,igrid,midg 1.9605757E-08 1.0112359E-08 1,midg,midg; igrid,midg,midg 5.5728875E-09 2.7113042E-08 gauss-seidel spectral radius is 0.9871380 estimated iterations to convergence 72 setup time was (sec) 0.3800000 now iterating at: 23:32:08 rms-change max change #iterations 0.1261401 20.76635 at 10iterations 1.2321802E-02 2.192995 at 20iterations 1.4158422E-03 0.2098694 at 30iterations 2.7916039E-04 4.8158646E-02 at 40iterations 8.9678935E-05 1.5375137E-02 at 50iterations finished qdiffx linear iterations at : 23:32:11 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 8.9678935E-05 1.5375137E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 23:32:12 3.526u 0.206s 0:04.10 90.7% 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 23:32:12 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 = 2390 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.904660 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): 80.70200 122.8590 ymin,ymax (A): 65.73300 121.8060 zmin,zma (A): 54.93100 108.3570 x,y,z range (A): 42.15701 56.07300 53.42600 scale (grids/A): 1.904660 object centre (A): 101.7805 93.76950 81.64400 number of atom coordinates read : 2390 total number of charged atoms : 2255 net assigned charge : 11.50002 assigned positive charge : 347.7543 centred at (gu) : 93.15506 87.97730 88.36735 assigned negative charge : -336.2551 centred at (gu) : 92.90182 88.07012 88.32915 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 70954 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21998 grid for indexing accessible points = 1.400000 m= 26810 mr = 48080 m= 4723 mr = 19711 m= 332 mr = 2924 m= 6 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 557 time to turn everything in is 0.3900000 number of dielectric boundary points 31963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 17759 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) : 0.6348867 object centre at (A) : 101.7805 93.76950 81.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9913302E-02 3.6037523E-02 midg,1,midg; midg,igrid,midg 3.6413852E-02 5.4595355E-02 1,midg,midg; igrid,midg,midg 2.4358341E-03 3.4082670E-02 gauss-seidel spectral radius is 0.9986240 estimated iterations to convergence 214 setup time was (sec) 0.6200000 now iterating at: 23:32:13 rms-change max change #iterations 3.907771 181.1829 at 10iterations 1.824361 71.51634 at 20iterations 0.8520906 29.32455 at 30iterations 0.3951508 12.45092 at 40iterations 0.1842823 6.262548 at 50iterations 8.5917450E-02 2.695669 at 60iterations 4.0275615E-02 1.288483 at 70iterations 1.8840026E-02 0.5971909 at 80iterations 8.8557778E-03 0.2913876 at 90iterations 4.1651330E-03 0.1326526 at 100iterations 1.9928182E-03 6.8817139E-02 at 110iterations 9.7882166E-04 3.9033890E-02 at 120iterations finished qdiffx linear iterations at : 23:32:20 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 9.7882166E-04 3.9033890E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 23:32:21 7.910u 0.597s 0:08.88 95.7% 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 23:32:21 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 = 2390 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.856990 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): 80.70200 122.8590 ymin,ymax (A): 65.73300 121.8060 zmin,zma (A): 54.93100 108.3570 x,y,z range (A): 42.15701 56.07300 53.42600 scale (grids/A): 2.856990 object centre (A): 101.7805 93.76950 81.64400 number of atom coordinates read : 2390 total number of charged atoms : 2255 net assigned charge : 11.50002 assigned positive charge : 347.7543 centred at (gu) : 94.73241 86.96588 87.55085 assigned negative charge : -336.2551 centred at (gu) : 94.35269 87.10525 87.49374 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 163796 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21998 grid for indexing accessible points = 1.400000 m= 84571 mr = 116726 m= 32814 mr = 68657 m= 8730 mr = 26394 m= 1415 mr = 6460 m= 113 mr = 943 m= 4 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 1625 time to turn everything in is 0.9400000 number of dielectric boundary points 72195 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 18040 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) : 1.904660 object centre at (A) : 101.7805 93.76950 81.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4885140 0.3839104 midg,1,midg; midg,igrid,midg 0.3937873 0.6695418 1,midg,midg; igrid,midg,midg 1.1859692E-02 0.3535305 gauss-seidel spectral radius is 0.9992610 estimated iterations to convergence 290 setup time was (sec) 1.170000 now iterating at: 23:32:22 rms-change max change #iterations 9.316246 382.5452 at 10iterations 5.464612 124.2234 at 20iterations 3.183381 66.91820 at 30iterations 1.855793 41.30644 at 40iterations 1.076336 22.03354 at 50iterations 0.6252704 13.52805 at 60iterations 0.3619047 7.404161 at 70iterations 0.2083136 4.020804 at 80iterations 0.1205774 2.453694 at 90iterations 6.9590472E-02 1.330691 at 100iterations 4.0099129E-02 0.7614861 at 110iterations 2.3070330E-02 0.5012016 at 120iterations 1.3330714E-02 0.2661271 at 130iterations 7.6954253E-03 0.1372881 at 140iterations 4.4399155E-03 8.9286804E-02 at 150iterations 2.5609345E-03 5.0354004E-02 at 160iterations 1.4895695E-03 2.9516220E-02 at 170iterations 8.6859771E-04 1.9248009E-02 at 180iterations finished qdiffx linear iterations at : 23:32:34 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 8.6859771E-04 1.9248009E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 23:32:34 12.707u 0.700s 0:13.69 97.8% 0+0k 0+0io 0pf+0w