Sun Oct 9 15:00:11 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 Sun Oct 9 2011 at 15:00:12 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 = 1137 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: 0.8583484 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): -63.19700 -21.72200 ymin,ymax (A): 23.16300 57.47400 zmin,zma (A): 11.14200 48.64600 x,y,z range (A): 41.47500 34.31100 37.50400 scale (grids/A): 0.8583484 object centre (A): -42.45950 40.31850 29.89400 number of atom coordinates read : 1137 total number of charged atoms : 1009 net assigned charge : 2.500005 assigned positive charge : 162.7672 centred at (gu) : 89.32039 91.68688 90.65911 assigned negative charge : -160.2671 centred at (gu) : 89.34854 91.78932 90.32064 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5924 nv = 96 ne = 84 npr = 23648 no. pairs analyzed = 23648 no. exposed pairs = 1488 no. arc points = 10572 no. surface atoms = 505 nbur = 632 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 534 mr = 3258 m= 5 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.2200000 number of dielectric boundary points 3070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 587 ## 51 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 5120 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.0353342E-07 1.9454972E-06 midg,1,midg; midg,igrid,midg 6.2322420E-07 -3.2417766E-08 1,midg,midg; igrid,midg,midg 5.7849422E-07 2.6139693E-07 gauss-seidel spectral radius is 0.9928104 estimated iterations to convergence 95 setup time was (sec) 0.4900000 now iterating at: 15:00:12 rms-change max change #iterations 0.2999701 39.64726 at 10iterations 5.2613866E-02 7.739498 at 20iterations 9.1699939E-03 1.195268 at 30iterations 1.5863471E-03 0.2090302 at 40iterations 2.8038706E-04 4.0491104E-02 at 50iterations finished qdiffx linear iterations at : 15:00:15 total time elapsed so far: 3.750000 # loops : 50 mean,max change (kT/e) : 2.8038706E-04 4.0491104E-02 energy calculations done at 3.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 15:00:16 3.933u 0.251s 0:04.47 93.5% 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 Sun Oct 9 2011 at 15:00:16 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 = 1137 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: 2.575045 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): -63.19700 -21.72200 ymin,ymax (A): 23.16300 57.47400 zmin,zma (A): 11.14200 48.64600 x,y,z range (A): 41.47500 34.31100 37.50400 scale (grids/A): 2.575045 object centre (A): -42.45950 40.31850 29.89400 number of atom coordinates read : 1137 total number of charged atoms : 1009 net assigned charge : 2.500005 assigned positive charge : 162.7672 centred at (gu) : 87.96153 95.06090 91.97755 assigned negative charge : -160.2671 centred at (gu) : 88.04571 95.36814 90.96205 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 60795 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10572 grid for indexing accessible points = 1.400000 m= 26385 mr = 41173 m= 7035 mr = 20397 m= 1059 mr = 5103 m= 93 mr = 653 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1634 time to turn everything in is 0.6000000 number of dielectric boundary points 27988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 8067 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) : 0.8583484 object centre at (A) : -42.45950 40.31850 29.89400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6795381E-02 8.1563070E-02 midg,1,midg; midg,igrid,midg 2.2672975E-02 -1.1452131E-02 1,midg,midg; igrid,midg,midg 2.1511649E-03 2.2258444E-02 gauss-seidel spectral radius is 0.9990665 estimated iterations to convergence 259 setup time was (sec) 0.9000000 now iterating at: 15:00:17 rms-change max change #iterations 4.483145 242.1987 at 10iterations 2.394972 94.99013 at 20iterations 1.274785 42.09626 at 30iterations 0.6805693 23.94484 at 40iterations 0.3626402 11.69855 at 50iterations 0.1934101 6.347810 at 60iterations 0.1031112 3.151406 at 70iterations 5.5103086E-02 1.523955 at 80iterations 2.9326694E-02 0.9401455 at 90iterations 1.5686460E-02 0.5079565 at 100iterations 8.3480151E-03 0.2696495 at 110iterations 4.4415630E-03 0.1509819 at 120iterations finished qdiffx linear iterations at : 15:00:25 total time elapsed so far: 9.050000 # loops : 120 mean,max change (kT/e) : 4.4415630E-03 0.1509819 energy calculations done at 9.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.230000 DelPhi exited at 15:00:26 9.232u 0.284s 0:09.81 96.9% 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 Sun Oct 9 2011 at 15:00:26 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 = 1137 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: 3.862568 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): -63.19700 -21.72200 ymin,ymax (A): 23.16300 57.47400 zmin,zma (A): 11.14200 48.64600 x,y,z range (A): 41.47500 34.31100 37.50400 scale (grids/A): 3.862568 object centre (A): -42.45950 40.31850 29.89400 number of atom coordinates read : 1137 total number of charged atoms : 1009 net assigned charge : 2.500005 assigned positive charge : 162.7672 centred at (gu) : 86.94226 97.59136 92.96640 assigned negative charge : -160.2671 centred at (gu) : 87.06846 98.05222 91.44312 start vw surface at 0.1200000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 139243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10572 grid for indexing accessible points = 1.400000 m= 77106 mr = 98411 m= 37633 mr = 64531 m= 14093 mr = 31685 m= 3979 mr = 11465 m= 856 mr = 3163 m= 133 mr = 630 m= 6 mr = 107 m= 0 mr = 3 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 5546 time to turn everything in is 1.960000 number of dielectric boundary points 63054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 8072 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) : 2.575045 object centre at (A) : -42.45950 40.31850 29.89400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4306554 0.3967951 midg,1,midg; midg,igrid,midg 5.5893004E-02 -0.1976700 1,midg,midg; igrid,midg,midg -0.1155528 0.1941156 gauss-seidel spectral radius is 0.9993368 estimated iterations to convergence 306 setup time was (sec) 2.270000 now iterating at: 15:00:28 rms-change max change #iterations 9.209317 231.5070 at 10iterations 5.472761 114.4975 at 20iterations 3.249405 62.00703 at 30iterations 1.929709 37.46557 at 40iterations 1.146944 21.32623 at 50iterations 0.6792736 11.62370 at 60iterations 0.4026669 7.349808 at 70iterations 0.2386626 4.571743 at 80iterations 0.1410673 2.306102 at 90iterations 8.3768710E-02 1.658171 at 100iterations 4.9639050E-02 1.046115 at 110iterations 2.9308809E-02 0.5219851 at 120iterations 1.7341785E-02 0.3156204 at 130iterations 1.0279092E-02 0.1915331 at 140iterations 6.0805152E-03 9.8936081E-02 at 150iterations 3.5943009E-03 6.6566467E-02 at 160iterations 2.1263384E-03 3.7890911E-02 at 170iterations 1.2577464E-03 2.2554994E-02 at 180iterations finished qdiffx linear iterations at : 15:00:42 total time elapsed so far: 15.56000 # loops : 180 mean,max change (kT/e) : 1.2577464E-03 2.2554994E-02 energy calculations done at 15.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.74000 DelPhi exited at 15:00:42 15.739u 0.308s 0:16.31 98.2% 0+0k 0+0io 0pf+0w