Tue Oct 11 08:33:49 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 08:33:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2857 !!! WARNING: ASP 30 has a net charge of -0.2720 !!! WARNING: LEU 297 has a net charge of -0.2720 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: 0.6564752 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): -12.27300 37.14200 ymin,ymax (A): 0.9780000 51.92900 zmin,zma (A): -8.476000 45.75300 x,y,z range (A): 49.41500 50.95100 54.22900 scale (grids/A): 0.6564752 object centre (A): 12.43450 26.45350 18.63850 number of atom coordinates read : 2857 total number of charged atoms : 2709 net assigned charge : 6.956024 assigned positive charge : 432.7086 centred at (gu) : 90.11612 90.94851 91.05097 assigned negative charge : -425.7532 centred at (gu) : 89.88731 90.77081 91.14858 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8379 nv = 96 ne = 84 npr = 57480 no. pairs analyzed = 57480 no. exposed pairs = 3453 no. arc points = 24294 no. surface atoms = 1161 nbur = 1696 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 459 mr = 4794 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.3600000 number of dielectric boundary points 3989 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2400 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9813 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8210746E-08 -4.7485589E-09 midg,1,midg; midg,igrid,midg -1.6124559E-08 6.1605398E-08 1,midg,midg; igrid,midg,midg -2.9701663E-08 6.1614280E-08 gauss-seidel spectral radius is 0.9879974 estimated iterations to convergence 75 setup time was (sec) 0.6600000 now iterating at: 08:34:07 rms-change max change #iterations 0.1679916 20.92558 at 10iterations 1.8253757E-02 2.309162 at 20iterations 1.9346451E-03 0.2500610 at 30iterations 2.0718973E-04 2.6630402E-02 at 40iterations 2.4940140E-05 2.9373169E-03 at 50iterations finished qdiffx linear iterations at : 08:34:11 total time elapsed so far: 5.160000 # loops : 50 mean,max change (kT/e) : 2.4940140E-05 2.9373169E-03 energy calculations done at 5.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.320000 DelPhi exited at 08:34:12 5.326u 0.484s 0:22.36 25.9% 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 Tue Oct 11 2011 at 08:34:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2857 !!! WARNING: ASP 30 has a net charge of -0.2720 !!! WARNING: LEU 297 has a net charge of -0.2720 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: 1.969426 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): -12.27300 37.14200 ymin,ymax (A): 0.9780000 51.92900 zmin,zma (A): -8.476000 45.75300 x,y,z range (A): 49.41500 50.95100 54.22900 scale (grids/A): 1.969426 object centre (A): 12.43450 26.45350 18.63850 number of atom coordinates read : 2857 total number of charged atoms : 2709 net assigned charge : 6.956024 assigned positive charge : 432.7086 centred at (gu) : 90.34782 92.84492 93.15174 assigned negative charge : -425.7532 centred at (gu) : 89.66163 92.31196 93.44529 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89607 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24294 grid for indexing accessible points = 1.400000 m= 34566 mr = 63385 m= 5847 mr = 26342 m= 360 mr = 3741 m= 3 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 450 time to turn everything in is 0.7800000 number of dielectric boundary points 36786 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 21363 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) : 0.6564752 object centre at (A) : 12.43450 26.45350 18.63850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5000729E-02 -1.6718289E-03 midg,1,midg; midg,igrid,midg -1.5180315E-02 4.6885584E-02 1,midg,midg; igrid,midg,midg -3.3668178E-04 7.1425132E-02 gauss-seidel spectral radius is 0.9987476 estimated iterations to convergence 224 setup time was (sec) 1.130000 now iterating at: 08:34:15 rms-change max change #iterations 4.797192 219.9773 at 10iterations 2.332108 83.31034 at 20iterations 1.125829 32.75270 at 30iterations 0.5453182 16.29541 at 40iterations 0.2649652 7.718666 at 50iterations 0.1284253 3.529144 at 60iterations 6.2058292E-02 1.664488 at 70iterations 3.0101797E-02 0.8112721 at 80iterations 1.4565795E-02 0.4255482 at 90iterations 7.0376643E-03 0.2193985 at 100iterations 3.4230999E-03 9.9353790E-02 at 110iterations 1.6651094E-03 4.5304298E-02 at 120iterations finished qdiffx linear iterations at : 08:34:28 total time elapsed so far: 13.71000 # loops : 120 mean,max change (kT/e) : 1.6651094E-03 4.5304298E-02 energy calculations done at 13.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.88000 DelPhi exited at 08:34:29 13.886u 0.514s 0:16.85 85.4% 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 Tue Oct 11 2011 at 08:34:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2857 !!! WARNING: ASP 30 has a net charge of -0.2720 !!! WARNING: LEU 297 has a net charge of -0.2720 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: 2.954139 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): -12.27300 37.14200 ymin,ymax (A): 0.9780000 51.92900 zmin,zma (A): -8.476000 45.75300 x,y,z range (A): 49.41500 50.95100 54.22900 scale (grids/A): 2.954139 object centre (A): 12.43450 26.45350 18.63850 number of atom coordinates read : 2857 total number of charged atoms : 2709 net assigned charge : 6.956024 assigned positive charge : 432.7086 centred at (gu) : 90.52144 94.26721 94.72752 assigned negative charge : -425.7532 centred at (gu) : 89.49235 93.46793 95.16805 start vw surface at 0.1300000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 206704 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24294 grid for indexing accessible points = 1.400000 m= 110210 mr = 152775 m= 42463 mr = 91858 m= 10627 mr = 34925 m= 1597 mr = 8170 m= 90 mr = 1088 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 1596 time to turn everything in is 2.050000 number of dielectric boundary points 82840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 21672 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) : 1.969426 object centre at (A) : 12.43450 26.45350 18.63850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9814697E-02 0.1705245 midg,1,midg; midg,igrid,midg -0.1875291 0.5396644 1,midg,midg; igrid,midg,midg -8.7295761E-03 0.5498101 gauss-seidel spectral radius is 0.9992869 estimated iterations to convergence 295 setup time was (sec) 2.450000 now iterating at: 08:34:32 rms-change max change #iterations 10.94495 427.2198 at 10iterations 6.456219 144.6898 at 20iterations 3.782397 65.76476 at 30iterations 2.209626 39.78046 at 40iterations 1.293759 22.07071 at 50iterations 0.7564402 13.05294 at 60iterations 0.4412813 7.527156 at 70iterations 0.2573372 4.340235 at 80iterations 0.1498322 2.712473 at 90iterations 8.7171607E-02 1.495365 at 100iterations 5.0651997E-02 0.8533564 at 110iterations 2.9490110E-02 0.5114517 at 120iterations 1.7180780E-02 0.3209190 at 130iterations 9.9901957E-03 0.1635129 at 140iterations 5.8180001E-03 0.1031151 at 150iterations 3.3861785E-03 5.5459023E-02 at 160iterations 1.9717873E-03 3.3060074E-02 at 170iterations 1.1514960E-03 1.9866943E-02 at 180iterations finished qdiffx linear iterations at : 08:34:52 total time elapsed so far: 23.16000 # loops : 180 mean,max change (kT/e) : 1.1514960E-03 1.9866943E-02 energy calculations done at 23.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.32000 DelPhi exited at 08:34:53 23.322u 0.537s 0:24.24 98.3% 0+0k 0+0io 0pf+0w