Sun Oct 9 08:16:02 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 Sun Oct 9 2011 at 08:16:02 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5614 !!! WARNING: HIR 704 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5357895 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): -17.03900 49.08600 ymin,ymax (A): 4.874000 71.31800 zmin,zma (A): -111.2860 -46.53200 x,y,z range (A): 66.12500 66.44400 64.75400 scale (grids/A): 0.5357895 object centre (A): 16.02350 38.09600 -78.90900 number of atom coordinates read : 5614 total number of charged atoms : 5446 net assigned charge : -2.985977 assigned positive charge : 847.6445 centred at (gu) : 90.43165 90.74880 89.34338 assigned negative charge : -850.6378 centred at (gu) : 90.42012 90.71409 89.24259 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 10435 nv = 96 ne = 84 npr = 111523 no. pairs analyzed = 111523 no. exposed pairs = 7282 no. arc points = 51317 no. surface atoms = 2438 nbur = 3176 mkacc time = 0.2000000 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= 477 mr = 5419 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 5468 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5078 ## 701 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 13861 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1829270E-09 6.2285815E-10 midg,1,midg; midg,igrid,midg -3.4833594E-10 2.1682464E-10 1,midg,midg; igrid,midg,midg -1.9719004E-10 -2.2640027E-11 gauss-seidel spectral radius is 0.9822516 estimated iterations to convergence 62 setup time was (sec) 0.5500000 now iterating at: 08:16:02 rms-change max change #iterations 9.8529883E-02 13.85994 at 10iterations 6.6265673E-03 0.8194752 at 20iterations 8.9006551E-04 0.1940384 at 30iterations 2.6256341E-04 6.0745239E-02 at 40iterations 8.9582427E-05 1.9954681E-02 at 50iterations finished qdiffx linear iterations at : 08:16:05 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 8.9582427E-05 1.9954681E-02 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 08:16:06 3.579u 0.166s 0:04.05 92.0% 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 08:16:06 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5614 !!! WARNING: HIR 704 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.607369 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): -17.03900 49.08600 ymin,ymax (A): 4.874000 71.31800 zmin,zma (A): -111.2860 -46.53200 x,y,z range (A): 66.12500 66.44400 64.75400 scale (grids/A): 1.607369 object centre (A): 16.02350 38.09600 -78.90900 number of atom coordinates read : 5614 total number of charged atoms : 5446 net assigned charge : -2.985977 assigned positive charge : 847.6445 centred at (gu) : 91.29326 92.24426 88.02811 assigned negative charge : -850.6378 centred at (gu) : 91.26012 92.14216 87.72707 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 115273 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51317 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 37249 mr = 78053 m= 4243 mr = 25529 m= 119 mr = 2171 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 563 time to turn everything in is 0.5500000 number of dielectric boundary points 51117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 631 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 41461 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) : 0.5357895 object centre at (A) : 16.02350 38.09600 -78.90900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1687664E-02 1.1633858E-02 midg,1,midg; midg,igrid,midg -8.7349666E-03 1.2415211E-02 1,midg,midg; igrid,midg,midg -2.4628730E-03 -1.2658488E-02 gauss-seidel spectral radius is 0.9983955 estimated iterations to convergence 198 setup time was (sec) 0.7800000 now iterating at: 08:16:07 rms-change max change #iterations 4.697322 167.8365 at 10iterations 2.051880 58.78829 at 20iterations 0.9028720 26.33725 at 30iterations 0.3972046 11.59091 at 40iterations 0.1750834 5.029711 at 50iterations 7.7020906E-02 2.241999 at 60iterations 3.3872534E-02 0.9476299 at 70iterations 1.4910999E-02 0.4326420 at 80iterations 6.6072335E-03 0.1808510 at 90iterations 2.9346496E-03 8.3362579E-02 at 100iterations 1.3096132E-03 3.7056923E-02 at 110iterations 5.9855991E-04 1.9952774E-02 at 120iterations finished qdiffx linear iterations at : 08:16:14 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 5.9855991E-04 1.9952774E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 08:16:14 8.186u 0.201s 0:08.73 95.9% 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 08:16:15 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5614 !!! WARNING: HIR 704 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.411053 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): -17.03900 49.08600 ymin,ymax (A): 4.874000 71.31800 zmin,zma (A): -111.2860 -46.53200 x,y,z range (A): 66.12500 66.44400 64.75400 scale (grids/A): 2.411053 object centre (A): 16.02350 38.09600 -78.90900 number of atom coordinates read : 5614 total number of charged atoms : 5446 net assigned charge : -2.985977 assigned positive charge : 847.6445 centred at (gu) : 91.93949 93.36585 87.04184 assigned negative charge : -850.6378 centred at (gu) : 91.88995 93.21313 86.59073 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 267149 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51317 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 126914 mr = 190972 m= 38272 mr = 99583 m= 6749 mr = 28737 m= 516 mr = 4628 m= 14 mr = 253 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 1893 time to turn everything in is 1.390000 number of dielectric boundary points 115441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 43493 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) : 1.607369 object centre at (A) : 16.02350 38.09600 -78.90900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8323453 0.1348108 midg,1,midg; midg,igrid,midg -7.9023294E-02 0.1720157 1,midg,midg; igrid,midg,midg -0.3404992 -0.1019443 gauss-seidel spectral radius is 0.9992737 estimated iterations to convergence 293 setup time was (sec) 1.640000 now iterating at: 08:16:16 rms-change max change #iterations 12.29282 435.5014 at 10iterations 7.350718 156.2859 at 20iterations 4.380762 91.70009 at 30iterations 2.592899 52.88353 at 40iterations 1.529771 33.61886 at 50iterations 0.9005117 16.13393 at 60iterations 0.5279475 9.352023 at 70iterations 0.3085115 6.100395 at 80iterations 0.1802762 3.215202 at 90iterations 0.1051971 1.992684 at 100iterations 6.1257187E-02 1.096551 at 110iterations 3.5671316E-02 0.5976492 at 120iterations 2.0735618E-02 0.3504181 at 130iterations 1.2061741E-02 0.2008966 at 140iterations 7.0060408E-03 0.1191435 at 150iterations 4.0721381E-03 6.8374634E-02 at 160iterations 2.3667752E-03 3.9743423E-02 at 170iterations 1.3760200E-03 2.3852348E-02 at 180iterations finished qdiffx linear iterations at : 08:16:29 total time elapsed so far: 13.94000 # loops : 180 mean,max change (kT/e) : 1.3760200E-03 2.3852348E-02 energy calculations done at 13.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.07000 DelPhi exited at 08:16:29 14.072u 0.220s 0:14.61 97.8% 0+0k 0+0io 0pf+0w