Sun Oct 9 07:55:34 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 07:55:35 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 208 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7062371 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): -16.39100 30.55900 ymin,ymax (A): -25.20300 25.20500 zmin,zma (A): -4.444000 34.59400 x,y,z range (A): 46.95000 50.40800 39.03800 scale (grids/A): 0.7062371 object centre (A): 7.084000 1.0004044E-03 15.07500 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000018 assigned positive charge : 332.2636 centred at (gu) : 90.00981 90.77583 90.78626 assigned negative charge : -326.2639 centred at (gu) : 89.89639 90.86787 90.91868 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7407 nv = 96 ne = 84 npr = 45763 no. pairs analyzed = 45763 no. exposed pairs = 2774 no. arc points = 19871 no. surface atoms = 938 nbur = 1273 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 444 mr = 4050 m= 5 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.2700000 number of dielectric boundary points 3732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1842 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8347 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9545971E-08 -2.0715671E-08 midg,1,midg; midg,igrid,midg 8.2738872E-08 3.6007390E-09 1,midg,midg; igrid,midg,midg -7.4099002E-09 1.0683645E-07 gauss-seidel spectral radius is 0.9895663 estimated iterations to convergence 80 setup time was (sec) 0.4800000 now iterating at: 07:55:35 rms-change max change #iterations 0.2005799 31.25815 at 10iterations 2.5012886E-02 3.569185 at 20iterations 3.0595087E-03 0.4387217 at 30iterations 3.7714065E-04 6.4631104E-02 at 40iterations 4.6105877E-05 5.7258606E-03 at 50iterations finished qdiffx linear iterations at : 07:55:38 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 4.6105877E-05 5.7258606E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 07:55:38 3.060u 0.140s 0:03.46 92.4% 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 07:55:38 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 208 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.118711 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): -16.39100 30.55900 ymin,ymax (A): -25.20300 25.20500 zmin,zma (A): -4.444000 34.59400 x,y,z range (A): 46.95000 50.40800 39.03800 scale (grids/A): 2.118711 object centre (A): 7.084000 1.0004044E-03 15.07500 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000018 assigned positive charge : 332.2636 centred at (gu) : 90.02909 92.32716 92.35858 assigned negative charge : -326.2639 centred at (gu) : 89.68880 92.60352 92.75588 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 78297 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19871 grid for indexing accessible points = 1.400000 m= 30466 mr = 53926 m= 5985 mr = 22722 m= 578 mr = 3938 m= 24 mr = 287 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1717 time to turn everything in is 0.6000000 number of dielectric boundary points 34474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 16464 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) : 0.7062371 object centre at (A) : 7.084000 1.0004044E-03 15.07500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8450235E-02 1.1154079E-02 midg,1,midg; midg,igrid,midg 3.7104066E-02 2.3368189E-02 1,midg,midg; igrid,midg,midg -1.4689977E-02 3.5386261E-02 gauss-seidel spectral radius is 0.9988450 estimated iterations to convergence 233 setup time was (sec) 0.9100000 now iterating at: 07:55:39 rms-change max change #iterations 4.827868 244.0473 at 10iterations 2.383039 76.07994 at 20iterations 1.185806 35.67698 at 30iterations 0.5896448 17.43436 at 40iterations 0.2930379 8.715576 at 50iterations 0.1457716 4.488174 at 60iterations 7.2643384E-02 2.315764 at 70iterations 3.6114525E-02 1.015087 at 80iterations 1.8014535E-02 0.5002289 at 90iterations 8.9285541E-03 0.2781029 at 100iterations 4.4538104E-03 0.1234884 at 110iterations 2.2114124E-03 6.3987732E-02 at 120iterations finished qdiffx linear iterations at : 07:55:46 total time elapsed so far: 7.910000 # loops : 120 mean,max change (kT/e) : 2.2114124E-03 6.3987732E-02 energy calculations done at 7.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.080000 DelPhi exited at 07:55:47 8.080u 0.255s 0:08.60 96.8% 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 07:55:47 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 208 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.178067 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): -16.39100 30.55900 ymin,ymax (A): -25.20300 25.20500 zmin,zma (A): -4.444000 34.59400 x,y,z range (A): 46.95000 50.40800 39.03800 scale (grids/A): 3.178067 object centre (A): 7.084000 1.0004044E-03 15.07500 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000018 assigned positive charge : 332.2636 centred at (gu) : 90.04370 93.49072 93.53796 assigned negative charge : -326.2639 centred at (gu) : 89.53322 93.90511 94.13393 start vw surface at 0.1300000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 180306 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19871 grid for indexing accessible points = 1.400000 m= 94558 mr = 129962 m= 38778 mr = 77660 m= 11385 mr = 31716 m= 2328 mr = 8703 m= 293 mr = 1648 m= 13 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.8799999 no. cavity mid-points inaccessible to solvent = 5717 time to turn everything in is 1.830000 number of dielectric boundary points 77807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 16592 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) : 2.118711 object centre at (A) : 7.084000 1.0004044E-03 15.07500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6280208 0.1231542 midg,1,midg; midg,igrid,midg 0.2486682 0.3568512 1,midg,midg; igrid,midg,midg -7.6353349E-02 0.2264900 gauss-seidel spectral radius is 0.9992967 estimated iterations to convergence 298 setup time was (sec) 2.160000 now iterating at: 07:55:49 rms-change max change #iterations 10.56144 423.8386 at 10iterations 6.174039 142.1131 at 20iterations 3.608622 69.27522 at 30iterations 2.110034 51.43016 at 40iterations 1.230815 21.35005 at 50iterations 0.7197587 14.22547 at 60iterations 0.4195808 7.656139 at 70iterations 0.2444999 4.239288 at 80iterations 0.1420389 2.417023 at 90iterations 8.2923561E-02 1.514320 at 100iterations 4.8284050E-02 0.8541164 at 110iterations 2.8098788E-02 0.4729404 at 120iterations 1.6374020E-02 0.2963839 at 130iterations 9.5375255E-03 0.1782665 at 140iterations 5.5484213E-03 9.3886375E-02 at 150iterations 3.2271422E-03 6.2278748E-02 at 160iterations 1.8808811E-03 3.1229019E-02 at 170iterations 1.0954979E-03 1.8544734E-02 at 180iterations finished qdiffx linear iterations at : 07:56:01 total time elapsed so far: 13.64000 # loops : 180 mean,max change (kT/e) : 1.0954979E-03 1.8544734E-02 energy calculations done at 13.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.82000 DelPhi exited at 07:56:01 13.822u 0.286s 0:14.37 98.1% 0+0k 0+0io 0pf+0w