Wed Dec 21 14:23:08 PST 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 Wed Dec 21 2011 at 14:23:09 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 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: 0.6013818 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): -23.75900 35.43800 ymin,ymax (A): -18.64500 20.54400 zmin,zma (A): -3.083000 38.59600 x,y,z range (A): 59.19700 39.18900 41.67900 scale (grids/A): 0.6013818 object centre (A): 5.839500 0.9494991 17.75650 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 2.000005 assigned positive charge : 289.5140 centred at (gu) : 89.59409 90.14214 90.20808 assigned negative charge : -287.5143 centred at (gu) : 89.61127 90.24066 90.36206 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4714 nv = 96 ne = 84 npr = 40037 no. pairs analyzed = 40037 no. exposed pairs = 2422 no. arc points = 17054 no. surface atoms = 820 nbur = 1126 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 196 mr = 2556 m= 0 mr = 8 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3300000 number of dielectric boundary points 2346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1707 ## 169 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 5783 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9433946E-09 -3.6858645E-09 midg,1,midg; midg,igrid,midg 3.5469367E-09 -1.9636854E-09 1,midg,midg; igrid,midg,midg 1.5310141E-09 3.9389081E-10 gauss-seidel spectral radius is 0.9856334 estimated iterations to convergence 68 setup time was (sec) 0.8100000 now iterating at: 14:23:10 rms-change max change #iterations 9.7356722E-02 20.10896 at 10iterations 8.4320707E-03 1.380193 at 20iterations 6.9346250E-04 0.1129169 at 30iterations 6.0805589E-05 9.9372864E-03 at 40iterations 5.0451908E-06 9.2697144E-04 at 50iterations finished qdiffx linear iterations at : 14:23:15 total time elapsed so far: 5.650000 # loops : 50 mean,max change (kT/e) : 5.0451908E-06 9.2697144E-04 energy calculations done at 5.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.860000 DelPhi exited at 14:23:16 5.867u 0.623s 0:07.47 86.7% 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 Wed Dec 21 2011 at 14:23:16 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 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: 1.804146 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): -23.75900 35.43800 ymin,ymax (A): -18.64500 20.54400 zmin,zma (A): -3.083000 38.59600 x,y,z range (A): 59.19700 39.18900 41.67900 scale (grids/A): 1.804146 object centre (A): 5.839500 0.9494991 17.75650 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 2.000005 assigned positive charge : 289.5140 centred at (gu) : 88.78233 90.42642 90.62404 assigned negative charge : -287.5143 centred at (gu) : 88.83391 90.72207 91.08640 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 51718 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17054 grid for indexing accessible points = 1.400000 m= 18033 mr = 35566 m= 2221 mr = 13427 m= 73 mr = 1362 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 2026 time to turn everything in is 0.5800000 number of dielectric boundary points 21685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 14173 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) : 0.6013818 object centre at (A) : 5.839500 0.9494991 17.75650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3421135E-03 -6.6607422E-03 midg,1,midg; midg,igrid,midg 2.0015088E-03 -5.2360771E-03 1,midg,midg; igrid,midg,midg 3.8248315E-02 3.1680983E-02 gauss-seidel spectral radius is 0.9984015 estimated iterations to convergence 198 setup time was (sec) 1.050000 now iterating at: 14:23:18 rms-change max change #iterations 3.266377 158.6646 at 10iterations 1.430353 62.39045 at 20iterations 0.6320280 27.85026 at 30iterations 0.2775020 10.42222 at 40iterations 0.1220324 4.783676 at 50iterations 5.3607978E-02 2.117897 at 60iterations 2.3577899E-02 1.026913 at 70iterations 1.0367278E-02 0.4178619 at 80iterations 4.5613912E-03 0.1751842 at 90iterations 2.0059065E-03 8.5265160E-02 at 100iterations 8.7936060E-04 3.5611153E-02 at 110iterations 3.8749829E-04 1.5377045E-02 at 120iterations finished qdiffx linear iterations at : 14:23:32 total time elapsed so far: 15.28000 # loops : 120 mean,max change (kT/e) : 3.8749829E-04 1.5377045E-02 energy calculations done at 15.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.51000 DelPhi exited at 14:23:33 15.514u 0.709s 0:16.60 97.6% 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 Wed Dec 21 2011 at 14:23:33 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 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: 2.706218 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): -23.75900 35.43800 ymin,ymax (A): -18.64500 20.54400 zmin,zma (A): -3.083000 38.59600 x,y,z range (A): 59.19700 39.18900 41.67900 scale (grids/A): 2.706218 object centre (A): 5.839500 0.9494991 17.75650 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 2.000005 assigned positive charge : 289.5140 centred at (gu) : 88.17334 90.63970 90.93613 assigned negative charge : -287.5143 centred at (gu) : 88.25102 91.08318 91.62961 start vw surface at 0.1300000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 119627 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17054 grid for indexing accessible points = 1.400000 m= 59507 mr = 86024 m= 19726 mr = 49102 m= 3843 mr = 15943 m= 275 mr = 2917 m= 10 mr = 126 m= 0 mr = 1 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 6858 time to turn everything in is 1.470000 number of dielectric boundary points 48875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 14512 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) : 1.804146 object centre at (A) : 5.839500 0.9494991 17.75650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1779519E-02 -5.5131439E-02 midg,1,midg; midg,igrid,midg 1.2742770E-02 -4.3281868E-02 1,midg,midg; igrid,midg,midg 0.4552220 0.3266762 gauss-seidel spectral radius is 0.9991747 estimated iterations to convergence 275 setup time was (sec) 1.990000 now iterating at: 14:23:35 rms-change max change #iterations 7.819921 293.4316 at 10iterations 4.375709 110.3442 at 20iterations 2.440820 57.17460 at 30iterations 1.357802 33.76462 at 40iterations 0.7551386 18.20306 at 50iterations 0.4194095 10.42519 at 60iterations 0.2330877 5.532707 at 70iterations 0.1294682 2.805194 at 80iterations 7.1819372E-02 1.505628 at 90iterations 3.9936408E-02 0.8621409 at 100iterations 2.2198789E-02 0.4589958 at 110iterations 1.2318062E-02 0.2575364 at 120iterations 6.8389699E-03 0.1592439 at 130iterations 3.7905888E-03 7.9012394E-02 at 140iterations 2.1104207E-03 4.4996262E-02 at 150iterations 1.1725130E-03 2.5859833E-02 at 160iterations 6.5079104E-04 1.5975952E-02 at 170iterations 3.6102938E-04 7.7419281E-03 at 180iterations finished qdiffx linear iterations at : 14:24:01 total time elapsed so far: 27.43000 # loops : 180 mean,max change (kT/e) : 3.6102938E-04 7.7419281E-03 energy calculations done at 27.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 27.66000 DelPhi exited at 14:24:02 27.660u 0.759s 0:28.72 98.9% 0+0k 0+0io 0pf+0w