Tue Oct 11 06:35:46 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 06:35:47 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2077 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7107774 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): -20.83400 23.85900 ymin,ymax (A): -28.61700 10.96900 zmin,zma (A): -13.45800 36.62800 x,y,z range (A): 44.69300 39.58600 50.08600 scale (grids/A): 0.7107774 object centre (A): 1.512501 -8.824000 11.58500 number of atom coordinates read : 2077 total number of charged atoms : 1943 net assigned charge : 5.931010 assigned positive charge : 314.7340 centred at (gu) : 90.51212 90.67275 89.22811 assigned negative charge : -308.8031 centred at (gu) : 90.36376 90.65471 89.15870 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7112 nv = 96 ne = 84 npr = 41840 no. pairs analyzed = 41840 no. exposed pairs = 2473 no. arc points = 16792 no. surface atoms = 847 nbur = 1230 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 459 mr = 4163 m= 7 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1597 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7911 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9414651E-08 7.7887293E-08 midg,1,midg; midg,igrid,midg 3.9262790E-08 7.2062910E-08 1,midg,midg; igrid,midg,midg -2.2596355E-08 1.4465580E-07 gauss-seidel spectral radius is 0.9896798 estimated iterations to convergence 80 setup time was (sec) 0.3600000 now iterating at: 06:35:47 rms-change max change #iterations 0.2074050 31.44811 at 10iterations 2.6437979E-02 3.599755 at 20iterations 3.5127050E-03 0.4135779 at 30iterations 5.6696864E-04 7.3528290E-02 at 40iterations 1.3055892E-04 1.7446518E-02 at 50iterations finished qdiffx linear iterations at : 06:35:50 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.3055892E-04 1.7446518E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 06:35:50 3.335u 0.163s 0:03.88 89.9% 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 Tue Oct 11 2011 at 06:35:50 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2077 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.132332 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): -20.83400 23.85900 ymin,ymax (A): -28.61700 10.96900 zmin,zma (A): -13.45800 36.62800 x,y,z range (A): 44.69300 39.58600 50.08600 scale (grids/A): 2.132332 object centre (A): 1.512501 -8.824000 11.58500 number of atom coordinates read : 2077 total number of charged atoms : 1943 net assigned charge : 5.931010 assigned positive charge : 314.7340 centred at (gu) : 91.53645 92.01829 87.68426 assigned negative charge : -308.8031 centred at (gu) : 91.09131 91.96402 87.47625 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 75747 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16792 grid for indexing accessible points = 1.400000 m= 30294 mr = 54356 m= 5952 mr = 23079 m= 571 mr = 4013 m= 13 mr = 306 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 30821 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 84 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 15424 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) : 0.7107774 object centre at (A) : 1.512501 -8.824000 11.58500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5041790E-02 4.4706848E-02 midg,1,midg; midg,igrid,midg 4.3486417E-03 3.0722825E-02 1,midg,midg; igrid,midg,midg 1.2019764E-02 3.9336760E-02 gauss-seidel spectral radius is 0.9988386 estimated iterations to convergence 232 setup time was (sec) 0.5900000 now iterating at: 06:35:51 rms-change max change #iterations 4.596880 187.7663 at 10iterations 2.273734 75.68820 at 20iterations 1.138761 33.72307 at 30iterations 0.5644189 18.31792 at 40iterations 0.2816317 8.749203 at 50iterations 0.1405983 4.118511 at 60iterations 6.9739237E-02 2.010502 at 70iterations 3.4804206E-02 1.021053 at 80iterations 1.7419668E-02 0.5254974 at 90iterations 8.7850839E-03 0.2778587 at 100iterations 4.4102934E-03 0.1308432 at 110iterations 2.2478451E-03 7.8559875E-02 at 120iterations finished qdiffx linear iterations at : 06:35:58 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 2.2478451E-03 7.8559875E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 06:35:59 7.735u 0.210s 0:08.22 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 Tue Oct 11 2011 at 06:35:59 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2077 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.198498 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): -20.83400 23.85900 ymin,ymax (A): -28.61700 10.96900 zmin,zma (A): -13.45800 36.62800 x,y,z range (A): 44.69300 39.58600 50.08600 scale (grids/A): 3.198498 object centre (A): 1.512501 -8.824000 11.58500 number of atom coordinates read : 2077 total number of charged atoms : 1943 net assigned charge : 5.931010 assigned positive charge : 314.7340 centred at (gu) : 92.30463 93.02751 86.52635 assigned negative charge : -308.8031 centred at (gu) : 91.63702 92.94605 86.21432 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 174544 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16792 grid for indexing accessible points = 1.400000 m= 94565 mr = 130549 m= 38376 mr = 78961 m= 11185 mr = 31751 m= 2223 mr = 8784 m= 291 mr = 1631 m= 9 mr = 174 m= 0 mr = 3 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.170000 number of dielectric boundary points 69340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 15544 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) : 2.132332 object centre at (A) : 1.512501 -8.824000 11.58500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5590476 0.3379583 midg,1,midg; midg,igrid,midg 1.5215865E-02 0.2454555 1,midg,midg; igrid,midg,midg 0.2110355 0.3290287 gauss-seidel spectral radius is 0.9992937 estimated iterations to convergence 297 setup time was (sec) 1.400000 now iterating at: 06:36:00 rms-change max change #iterations 10.22784 411.0341 at 10iterations 6.045816 122.9870 at 20iterations 3.558805 80.82054 at 30iterations 2.096690 48.95916 at 40iterations 1.233949 21.75341 at 50iterations 0.7247044 13.64935 at 60iterations 0.4247854 7.278248 at 70iterations 0.2490477 4.511171 at 80iterations 0.1459598 2.771215 at 90iterations 8.5759662E-02 1.464621 at 100iterations 5.0349221E-02 0.8502960 at 110iterations 2.9730776E-02 0.5711350 at 120iterations 1.7705562E-02 0.3270884 at 130iterations 1.0728272E-02 0.1927719 at 140iterations 6.6952016E-03 0.1213875 at 150iterations 4.3393192E-03 8.4857941E-02 at 160iterations 2.9757202E-03 6.1180115E-02 at 170iterations 2.1479358E-03 4.0737152E-02 at 180iterations finished qdiffx linear iterations at : 06:36:11 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 2.1479358E-03 4.0737152E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 06:36:12 12.693u 0.206s 0:13.42 96.0% 0+0k 0+0io 0pf+0w