Sun Oct 9 03:19:51 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 03:19:51 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4299 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5319945 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): 219.1840 275.7300 ymin,ymax (A): 72.78100 139.6990 zmin,zma (A): -69.86800 -7.884000 x,y,z range (A): 56.54597 66.91799 61.98400 scale (grids/A): 0.5319945 object centre (A): 247.4570 106.2400 -38.87600 number of atom coordinates read : 4299 total number of charged atoms : 4154 net assigned charge : 15.50000 assigned positive charge : 636.4943 centred at (gu) : 90.00227 87.73434 90.64787 assigned negative charge : -620.9989 centred at (gu) : 90.05054 87.74549 90.67870 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7752 nv = 96 ne = 84 npr = 86558 no. pairs analyzed = 86558 no. exposed pairs = 5533 no. arc points = 38151 no. surface atoms = 1895 nbur = 2404 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 335 mr = 3886 m= 0 mr = 12 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 4189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3834 ## 457 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10279 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0625677E-10 4.4386034E-10 midg,1,midg; midg,igrid,midg 1.0698006E-09 2.8132374E-10 1,midg,midg; igrid,midg,midg 8.0438151E-10 2.8474109E-10 gauss-seidel spectral radius is 0.9818964 estimated iterations to convergence 61 setup time was (sec) 0.6500000 now iterating at: 03:19:52 rms-change max change #iterations 7.7892430E-02 12.81736 at 10iterations 6.3735843E-03 0.8917141 at 20iterations 1.3989935E-03 0.1857491 at 30iterations 4.6568297E-04 6.3550949E-02 at 40iterations 1.5952585E-04 2.2354126E-02 at 50iterations finished qdiffx linear iterations at : 03:19:54 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.5952585E-04 2.2354126E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 03:19:55 3.323u 0.143s 0:03.77 91.7% 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 Sun Oct 9 2011 at 03:19:55 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4299 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.595983 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): 219.1840 275.7300 ymin,ymax (A): 72.78100 139.6990 zmin,zma (A): -69.86800 -7.884000 x,y,z range (A): 56.54597 66.91799 61.98400 scale (grids/A): 1.595983 object centre (A): 247.4570 106.2400 -38.87600 number of atom coordinates read : 4299 total number of charged atoms : 4154 net assigned charge : 15.50000 assigned positive charge : 636.4943 centred at (gu) : 90.00515 83.20134 91.94175 assigned negative charge : -620.9989 centred at (gu) : 90.15119 83.23602 92.03544 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 85171 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38151 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 27282 mr = 56621 m= 3035 mr = 18662 m= 75 mr = 1469 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 944 time to turn everything in is 0.5900000 number of dielectric boundary points 38807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 403 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 31589 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) : 0.5319945 object centre at (A) : 247.4570 106.2400 -38.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6059356E-02 8.7329466E-03 midg,1,midg; midg,igrid,midg 3.3275895E-02 1.3296661E-02 1,midg,midg; igrid,midg,midg 3.9930795E-03 6.9436320E-04 gauss-seidel spectral radius is 0.9982440 estimated iterations to convergence 190 setup time was (sec) 0.8800000 now iterating at: 03:19:56 rms-change max change #iterations 3.833936 149.3046 at 10iterations 1.614746 55.51644 at 20iterations 0.6827723 24.09727 at 30iterations 0.2886679 8.860987 at 40iterations 0.1223937 4.127042 at 50iterations 5.2061472E-02 1.780413 at 60iterations 2.2317255E-02 0.7059984 at 70iterations 9.7411927E-03 0.3126707 at 80iterations 4.4237347E-03 0.1442127 at 90iterations 2.1651553E-03 7.4835360E-02 at 100iterations 1.1699201E-03 3.6896706E-02 at 110iterations 7.0045335E-04 2.1106720E-02 at 120iterations finished qdiffx linear iterations at : 03:20:02 total time elapsed so far: 6.980000 # loops : 120 mean,max change (kT/e) : 7.0045335E-04 2.1106720E-02 energy calculations done at 6.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.160000 DelPhi exited at 03:20:02 7.165u 0.181s 0:07.67 95.6% 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 03:20:02 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4299 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: 2.393975 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): 219.1840 275.7300 ymin,ymax (A): 72.78100 139.6990 zmin,zma (A): -69.86800 -7.884000 x,y,z range (A): 56.54597 66.91799 61.98400 scale (grids/A): 2.393975 object centre (A): 247.4570 106.2400 -38.87600 number of atom coordinates read : 4299 total number of charged atoms : 4154 net assigned charge : 15.50000 assigned positive charge : 636.4943 centred at (gu) : 90.00718 79.80148 92.91244 assigned negative charge : -620.9989 centred at (gu) : 90.22669 79.85387 93.05312 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 197909 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38151 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 92382 mr = 139629 m= 28108 mr = 72078 m= 4663 mr = 20955 m= 326 mr = 3020 m= 10 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 3336 time to turn everything in is 1.440000 number of dielectric boundary points 87600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 33190 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) : 1.595983 object centre at (A) : 247.4570 106.2400 -38.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3782046 7.1281791E-02 midg,1,midg; midg,igrid,midg 0.5103211 0.1813118 1,midg,midg; igrid,midg,midg 8.6531922E-02 -1.4308389E-02 gauss-seidel spectral radius is 0.9991938 estimated iterations to convergence 278 setup time was (sec) 1.730000 now iterating at: 03:20:04 rms-change max change #iterations 10.19105 285.8791 at 10iterations 5.912513 148.3634 at 20iterations 3.407499 101.0730 at 30iterations 1.945652 44.95927 at 40iterations 1.109011 22.22219 at 50iterations 0.6282044 12.35164 at 60iterations 0.3560931 7.181383 at 70iterations 0.2011903 3.663630 at 80iterations 0.1136752 2.073662 at 90iterations 6.3941859E-02 1.183071 at 100iterations 3.5972651E-02 0.6859417 at 110iterations 2.0290492E-02 0.3729162 at 120iterations 1.1420172E-02 0.2067413 at 130iterations 6.4510806E-03 0.1252327 at 140iterations 3.6416850E-03 7.2929382E-02 at 150iterations 2.0735662E-03 3.6941528E-02 at 160iterations 1.1940672E-03 2.3597717E-02 at 170iterations 6.9823454E-04 1.2863159E-02 at 180iterations finished qdiffx linear iterations at : 03:20:14 total time elapsed so far: 11.60000 # loops : 180 mean,max change (kT/e) : 6.9823454E-04 1.2863159E-02 energy calculations done at 11.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.78000 DelPhi exited at 03:20:15 11.784u 0.221s 0:12.28 97.7% 0+0k 0+0io 0pf+0w