Mon Oct 10 00:13:30 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 Mon Oct 10 2011 at 00:13:31 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3088 !!! WARNING: SEP 140 has a net charge of -0.4750 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: 0.6291087 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): -19.55600 34.84600 ymin,ymax (A): -38.01900 13.11400 zmin,zma (A): -14.36100 42.22700 x,y,z range (A): 54.40200 51.13300 56.58800 scale (grids/A): 0.6291087 object centre (A): 7.645000 -12.45250 13.93300 number of atom coordinates read : 3088 total number of charged atoms : 2944 net assigned charge : 2.025009 assigned positive charge : 467.0540 centred at (gu) : 89.05653 89.58244 91.60938 assigned negative charge : -465.0302 centred at (gu) : 89.07571 89.67934 91.57352 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8148 nv = 96 ne = 84 npr = 61379 no. pairs analyzed = 61379 no. exposed pairs = 4032 no. arc points = 28515 no. surface atoms = 1344 nbur = 1744 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 390 mr = 4250 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.3600000 number of dielectric boundary points 4256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2887 ## 284 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 10037 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1660698E-09 8.0940721E-09 midg,1,midg; midg,igrid,midg 1.3024498E-08 -7.3582553E-09 1,midg,midg; igrid,midg,midg 4.8806994E-09 4.1771201E-11 gauss-seidel spectral radius is 0.9869615 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 00:13:31 rms-change max change #iterations 0.1449431 22.07522 at 10iterations 1.3894262E-02 2.069931 at 20iterations 1.3090296E-03 0.1671638 at 30iterations 1.2724580E-04 1.9523621E-02 at 40iterations 1.2751712E-05 1.6975403E-03 at 50iterations finished qdiffx linear iterations at : 00:13:34 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.2751712E-05 1.6975403E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 00:13:34 3.432u 0.131s 0:03.83 92.9% 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 Mon Oct 10 2011 at 00:13:34 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3088 !!! WARNING: SEP 140 has a net charge of -0.4750 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: 1.887326 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): -19.55600 34.84600 ymin,ymax (A): -38.01900 13.11400 zmin,zma (A): -14.36100 42.22700 x,y,z range (A): 54.40200 51.13300 56.58800 scale (grids/A): 1.887326 object centre (A): 7.645000 -12.45250 13.93300 number of atom coordinates read : 3088 total number of charged atoms : 2944 net assigned charge : 2.025009 assigned positive charge : 467.0540 centred at (gu) : 87.16889 88.74647 94.82728 assigned negative charge : -465.0302 centred at (gu) : 87.22678 89.03758 94.72041 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 88925 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28515 grid for indexing accessible points = 1.400000 m= 29378 mr = 60269 m= 4010 mr = 20695 m= 209 mr = 2272 m= 3 mr = 43 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2150 time to turn everything in is 0.6400000 number of dielectric boundary points 39247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 23164 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) : 0.6291087 object centre at (A) : 7.645000 -12.45250 13.93300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2232526E-02 3.0411626E-03 midg,1,midg; midg,igrid,midg 1.3177744E-02 -3.7392217E-03 1,midg,midg; igrid,midg,midg 6.4256717E-03 -1.5291822E-02 gauss-seidel spectral radius is 0.9986682 estimated iterations to convergence 217 setup time was (sec) 0.9300000 now iterating at: 00:13:36 rms-change max change #iterations 4.639777 184.7860 at 10iterations 2.184260 67.60612 at 20iterations 1.028475 35.58198 at 30iterations 0.4866062 14.59581 at 40iterations 0.2298641 6.943935 at 50iterations 0.1085068 3.190693 at 60iterations 5.1161617E-02 1.547077 at 70iterations 2.4220547E-02 0.7137413 at 80iterations 1.1387315E-02 0.3379427 at 90iterations 5.4089325E-03 0.1566501 at 100iterations 2.5476711E-03 8.2492828E-02 at 110iterations 1.2049780E-03 3.4145355E-02 at 120iterations finished qdiffx linear iterations at : 00:13:43 total time elapsed so far: 8.520000 # loops : 120 mean,max change (kT/e) : 1.2049780E-03 3.4145355E-02 energy calculations done at 8.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.740000 DelPhi exited at 00:13:44 8.738u 0.157s 0:09.21 96.4% 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 Mon Oct 10 2011 at 00:13:44 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3088 !!! WARNING: SEP 140 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.830989 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): -19.55600 34.84600 ymin,ymax (A): -38.01900 13.11400 zmin,zma (A): -14.36100 42.22700 x,y,z range (A): 54.40200 51.13300 56.58800 scale (grids/A): 2.830989 object centre (A): 7.645000 -12.45250 13.93300 number of atom coordinates read : 3088 total number of charged atoms : 2944 net assigned charge : 2.025009 assigned positive charge : 467.0540 centred at (gu) : 85.75325 88.11963 97.24091 assigned negative charge : -465.0302 centred at (gu) : 85.84006 88.55631 97.08064 start vw surface at 0.1600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 205963 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28515 grid for indexing accessible points = 1.400000 m= 98007 mr = 146993 m= 32026 mr = 78381 m= 6931 mr = 24655 m= 861 mr = 4854 m= 34 mr = 500 m= 0 mr = 2 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 6869 time to turn everything in is 1.580000 number of dielectric boundary points 88437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 23550 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) : 1.887326 object centre at (A) : 7.645000 -12.45250 13.93300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1400652 -4.6170402E-02 midg,1,midg; midg,igrid,midg -8.3382010E-02 4.4731718E-02 1,midg,midg; igrid,midg,midg -3.4596626E-02 -0.2826866 gauss-seidel spectral radius is 0.9992913 estimated iterations to convergence 296 setup time was (sec) 1.880000 now iterating at: 00:13:46 rms-change max change #iterations 11.12060 431.4320 at 10iterations 6.699298 143.9972 at 20iterations 3.992478 86.58558 at 30iterations 2.362092 44.92818 at 40iterations 1.395587 26.50329 at 50iterations 0.8198159 14.69318 at 60iterations 0.4815600 8.406882 at 70iterations 0.2816327 5.051529 at 80iterations 0.1645105 3.059852 at 90iterations 9.6016429E-02 1.599446 at 100iterations 5.5994194E-02 0.9791410 at 110iterations 3.2657444E-02 0.5656719 at 120iterations 1.9040156E-02 0.3113403 at 130iterations 1.1086939E-02 0.1957264 at 140iterations 6.4621503E-03 0.1134644 at 150iterations 3.7619662E-03 6.2718391E-02 at 160iterations 2.1921436E-03 3.5655975E-02 at 170iterations 1.2712387E-03 2.3403734E-02 at 180iterations finished qdiffx linear iterations at : 00:13:56 total time elapsed so far: 12.23000 # loops : 180 mean,max change (kT/e) : 1.2712387E-03 2.3403734E-02 energy calculations done at 12.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 00:13:57 12.422u 0.152s 0:12.84 97.8% 0+0k 0+0io 0pf+0w