Sat Oct 15 11:29:26 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 Sat Oct 15 2011 at 11:29:26 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 466 has a net charge of 1.4000 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: 0.6229767 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): -31.92000 17.53200 ymin,ymax (A): -23.99900 22.77300 zmin,zma (A): -12.13100 45.01400 x,y,z range (A): 49.45200 46.77200 57.14500 scale (grids/A): 0.6229767 object centre (A): -7.194000 -0.6130009 16.44150 number of atom coordinates read : 2586 total number of charged atoms : 2457 net assigned charge : 4.000009 assigned positive charge : 391.9970 centred at (gu) : 88.49221 89.14709 89.59014 assigned negative charge : -387.9975 centred at (gu) : 88.39491 89.17743 89.48589 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6612 nv = 96 ne = 84 npr = 53529 no. pairs analyzed = 53529 no. exposed pairs = 3008 no. arc points = 21696 no. surface atoms = 1011 nbur = 1575 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 361 mr = 3706 m= 3 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.3100000 number of dielectric boundary points 3214 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2226 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8212 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3561603E-09 1.0137462E-08 midg,1,midg; midg,igrid,midg 7.0267729E-09 1.2357172E-09 1,midg,midg; igrid,midg,midg -4.9307900E-09 7.6356166E-09 gauss-seidel spectral radius is 0.9866515 estimated iterations to convergence 71 setup time was (sec) 0.6400000 now iterating at: 11:29:27 rms-change max change #iterations 0.1320647 19.96714 at 10iterations 1.2106541E-02 1.900928 at 20iterations 1.1272317E-03 0.1823540 at 30iterations 1.0496798E-04 1.6675949E-02 at 40iterations 9.9518320E-06 1.3809204E-03 at 50iterations finished qdiffx linear iterations at : 11:29:31 total time elapsed so far: 5.070000 # loops : 50 mean,max change (kT/e) : 9.9518320E-06 1.3809204E-03 energy calculations done at 5.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.240000 DelPhi exited at 11:29:32 5.241u 0.476s 0:06.27 91.0% 0+0k 0+0io 6pf+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 Sat Oct 15 2011 at 11:29:32 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 466 has a net charge of 1.4000 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: 1.868930 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): -31.92000 17.53200 ymin,ymax (A): -23.99900 22.77300 zmin,zma (A): -12.13100 45.01400 x,y,z range (A): 49.45200 46.77200 57.14500 scale (grids/A): 1.868930 object centre (A): -7.194000 -0.6130009 16.44150 number of atom coordinates read : 2586 total number of charged atoms : 2457 net assigned charge : 4.000009 assigned positive charge : 391.9970 centred at (gu) : 85.47619 87.44092 88.76945 assigned negative charge : -387.9975 centred at (gu) : 85.18453 87.53207 88.45742 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21696 grid for indexing accessible points = 1.400000 m= 25899 mr = 50507 m= 3887 mr = 19409 m= 213 mr = 2470 m= 3 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 4321 time to turn everything in is 0.6200000 number of dielectric boundary points 29533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 19278 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) : 0.6229767 object centre at (A) : -7.194000 -0.6130009 16.44150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8276321E-02 1.8998515E-02 midg,1,midg; midg,igrid,midg 1.1738284E-02 2.9618649E-03 1,midg,midg; igrid,midg,midg -5.2225348E-03 3.1956758E-02 gauss-seidel spectral radius is 0.9985797 estimated iterations to convergence 210 setup time was (sec) 1.030000 now iterating at: 11:29:34 rms-change max change #iterations 4.055431 147.3374 at 10iterations 1.874414 61.84939 at 20iterations 0.8647860 25.36928 at 30iterations 0.3975368 13.72587 at 40iterations 0.1837708 5.760981 at 50iterations 8.4784538E-02 2.614042 at 60iterations 3.9248515E-02 1.347811 at 70iterations 1.8089965E-02 0.6482239 at 80iterations 8.3448803E-03 0.2697296 at 90iterations 3.8539718E-03 0.1173954 at 100iterations 1.7794995E-03 6.6833496E-02 at 110iterations 8.2181563E-04 2.5538445E-02 at 120iterations finished qdiffx linear iterations at : 11:29:45 total time elapsed so far: 12.26000 # loops : 120 mean,max change (kT/e) : 8.2181563E-04 2.5538445E-02 energy calculations done at 12.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.43000 DelPhi exited at 11:29:46 12.435u 0.524s 0:13.48 96.0% 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 Sat Oct 15 2011 at 11:29:46 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 466 has a net charge of 1.4000 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: 2.803395 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): -31.92000 17.53200 ymin,ymax (A): -23.99900 22.77300 zmin,zma (A): -12.13100 45.01400 x,y,z range (A): 49.45200 46.77200 57.14500 scale (grids/A): 2.803395 object centre (A): -7.194000 -0.6130009 16.44150 number of atom coordinates read : 2586 total number of charged atoms : 2457 net assigned charge : 4.000009 assigned positive charge : 391.9970 centred at (gu) : 83.21414 86.16132 88.15408 assigned negative charge : -387.9975 centred at (gu) : 82.77668 86.29800 87.68606 start vw surface at 0.1100000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 166481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21696 grid for indexing accessible points = 1.400000 m= 84847 mr = 122072 m= 29869 mr = 70449 m= 7084 mr = 24162 m= 928 mr = 5455 m= 34 mr = 610 m= 0 mr = 9 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 14828 time to turn everything in is 1.560000 number of dielectric boundary points 66486 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 19655 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) : 1.868930 object centre at (A) : -7.194000 -0.6130009 16.44150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1115778 0.1494049 midg,1,midg; midg,igrid,midg 0.1565787 4.2018913E-02 1,midg,midg; igrid,midg,midg -4.0312614E-02 0.4021430 gauss-seidel spectral radius is 0.9992383 estimated iterations to convergence 286 setup time was (sec) 1.970000 now iterating at: 11:29:48 rms-change max change #iterations 9.519090 332.5033 at 10iterations 5.458785 103.8527 at 20iterations 3.108412 59.63717 at 30iterations 1.773616 34.07127 at 40iterations 1.009919 18.53662 at 50iterations 0.5752886 10.61230 at 60iterations 0.3276142 6.076965 at 70iterations 0.1866419 3.655355 at 80iterations 0.1061714 2.141232 at 90iterations 6.0342025E-02 1.067965 at 100iterations 3.4399930E-02 0.7296753 at 110iterations 1.9537911E-02 0.3464267 at 120iterations 1.1124740E-02 0.1954050 at 130iterations 6.3509108E-03 0.1193991 at 140iterations 3.6057152E-03 6.7588806E-02 at 150iterations 2.0517027E-03 3.9864540E-02 at 160iterations 1.1704520E-03 2.1711826E-02 at 170iterations 6.6530076E-04 1.2954712E-02 at 180iterations finished qdiffx linear iterations at : 11:30:08 total time elapsed so far: 21.85000 # loops : 180 mean,max change (kT/e) : 6.6530076E-04 1.2954712E-02 energy calculations done at 21.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.03000 DelPhi exited at 11:30:09 22.030u 0.583s 0:23.05 98.0% 0+0k 0+0io 0pf+0w