Tue Oct 11 06:02:03 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 Tue Oct 11 2011 at 06:02:03 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 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: 0.7295231 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): 25.62900 73.05800 ymin,ymax (A): -18.80000 29.99900 zmin,zma (A): 3.907000 46.37900 x,y,z range (A): 47.42900 48.79900 42.47200 scale (grids/A): 0.7295231 object centre (A): 49.34350 5.599501 25.14300 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 88.85366 90.55929 90.27871 assigned negative charge : -312.6442 centred at (gu) : 88.98309 90.51176 90.36466 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7707 nv = 96 ne = 84 npr = 41744 no. pairs analyzed = 41744 no. exposed pairs = 2578 no. arc points = 17685 no. surface atoms = 884 nbur = 1406 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 554 mr = 4503 m= 5 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1586 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8229 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4967956E-07 2.1291914E-08 midg,1,midg; midg,igrid,midg 4.6789477E-08 1.4143444E-07 1,midg,midg; igrid,midg,midg 2.3834367E-07 -1.0988709E-08 gauss-seidel spectral radius is 0.9902029 estimated iterations to convergence 82 setup time was (sec) 0.5300000 now iterating at: 06:02:04 rms-change max change #iterations 0.2251271 28.80949 at 10iterations 3.0502506E-02 3.844543 at 20iterations 4.2233393E-03 0.5121002 at 30iterations 7.5029064E-04 8.8691711E-02 at 40iterations 2.0624604E-04 2.3773193E-02 at 50iterations finished qdiffx linear iterations at : 06:02:07 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 2.0624604E-04 2.3773193E-02 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 06:02:08 3.141u 0.138s 0:05.17 63.2% 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 Tue Oct 11 2011 at 06:02:08 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 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: 2.188570 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): 25.62900 73.05800 ymin,ymax (A): -18.80000 29.99900 zmin,zma (A): 3.907000 46.37900 x,y,z range (A): 47.42900 48.79900 42.47200 scale (grids/A): 2.188570 object centre (A): 49.34350 5.599501 25.14300 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 86.56100 91.67795 90.83580 assigned negative charge : -312.6442 centred at (gu) : 86.94913 91.53554 91.09421 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17685 grid for indexing accessible points = 1.400000 m= 34441 mr = 58316 m= 7260 mr = 26440 m= 782 mr = 4999 m= 28 mr = 411 m= 0 mr = 3 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 33587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15660 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) : 0.7295231 object centre at (A) : 49.34350 5.599501 25.14300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5475765E-02 3.0371778E-02 midg,1,midg; midg,igrid,midg 5.3378414E-02 3.0926365E-02 1,midg,midg; igrid,midg,midg 5.7983093E-02 -4.1247103E-02 gauss-seidel spectral radius is 0.9988931 estimated iterations to convergence 238 setup time was (sec) 0.9000000 now iterating at: 06:02:10 rms-change max change #iterations 4.896248 189.3393 at 10iterations 2.462383 85.58798 at 20iterations 1.251176 37.27266 at 30iterations 0.6312441 18.76066 at 40iterations 0.3187911 8.951691 at 50iterations 0.1617100 4.670261 at 60iterations 8.1851140E-02 2.342978 at 70iterations 4.1461471E-02 1.202133 at 80iterations 2.1066524E-02 0.5742466 at 90iterations 1.0808865E-02 0.3336808 at 100iterations 5.5467910E-03 0.1544724 at 110iterations 2.9261829E-03 8.4114075E-02 at 120iterations finished qdiffx linear iterations at : 06:02:16 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 2.9261829E-03 8.4114075E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 06:02:17 7.787u 0.206s 0:08.59 92.8% 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 Tue Oct 11 2011 at 06:02:17 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 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: 3.282854 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): 25.62900 73.05800 ymin,ymax (A): -18.80000 29.99900 zmin,zma (A): 3.907000 46.37900 x,y,z range (A): 47.42900 48.79900 42.47200 scale (grids/A): 3.282854 object centre (A): 49.34350 5.599501 25.14300 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 84.84146 92.51699 91.25359 assigned negative charge : -312.6442 centred at (gu) : 85.42369 92.30328 91.64133 start vw surface at 0.1600000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 187048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17685 grid for indexing accessible points = 1.400000 m= 105104 mr = 139666 m= 45095 mr = 88142 m= 13866 mr = 37628 m= 3056 mr = 10989 m= 417 mr = 2203 m= 12 mr = 275 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.980000 number of dielectric boundary points 75695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 15752 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) : 2.188570 object centre at (A) : 49.34350 5.599501 25.14300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1169188 0.2455846 midg,1,midg; midg,igrid,midg 0.4137363 0.1764317 1,midg,midg; igrid,midg,midg 0.5395882 -0.4821947 gauss-seidel spectral radius is 0.9993151 estimated iterations to convergence 301 setup time was (sec) 2.300000 now iterating at: 06:02:20 rms-change max change #iterations 10.72798 360.5589 at 10iterations 6.417935 128.4193 at 20iterations 3.822995 74.24883 at 30iterations 2.283204 42.84708 at 40iterations 1.355929 27.34705 at 50iterations 0.8030168 15.24707 at 60iterations 0.4756409 7.836358 at 70iterations 0.2815385 4.656813 at 80iterations 0.1664477 2.910888 at 90iterations 9.8436788E-02 1.787865 at 100iterations 5.8097523E-02 0.9477539 at 110iterations 3.4591068E-02 0.5664775 at 120iterations 2.0660989E-02 0.4295483 at 130iterations 1.2487679E-02 0.2489548 at 140iterations 7.7369143E-03 0.1363468 at 150iterations 4.9638287E-03 8.8264465E-02 at 160iterations 3.3570749E-03 5.9104919E-02 at 170iterations 2.4183267E-03 4.2705536E-02 at 180iterations finished qdiffx linear iterations at : 06:02:30 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 2.4183267E-03 4.2705536E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 06:02:31 12.862u 0.317s 0:14.41 91.3% 0+0k 0+0io 0pf+0w