Sun Oct 9 14:07:11 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 Sun Oct 9 2011 at 14:07:12 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 = 2415 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6628682 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): -6.993000 42.21400 ymin,ymax (A): 21.61200 75.31800 zmin,zma (A): 41.78300 84.72800 x,y,z range (A): 49.20700 53.70600 42.94500 scale (grids/A): 0.6628682 object centre (A): 17.61050 48.46500 63.25550 number of atom coordinates read : 2415 total number of charged atoms : 2273 net assigned charge : 4.500021 assigned positive charge : 370.2409 centred at (gu) : 90.64062 90.85638 90.54340 assigned negative charge : -365.7415 centred at (gu) : 90.66341 90.97116 90.67809 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7031 nv = 96 ne = 84 npr = 48599 no. pairs analyzed = 48599 no. exposed pairs = 3051 no. arc points = 21637 no. surface atoms = 1027 nbur = 1388 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 387 mr = 3757 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2039 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8244 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5204252E-08 -1.6445394E-08 midg,1,midg; midg,igrid,midg 2.9762278E-08 -1.2725375E-08 1,midg,midg; igrid,midg,midg 1.5241548E-08 9.3124664E-09 gauss-seidel spectral radius is 0.9881857 estimated iterations to convergence 75 setup time was (sec) 0.3800000 now iterating at: 14:07:12 rms-change max change #iterations 0.1603846 25.55596 at 10iterations 1.7898502E-02 2.659058 at 20iterations 2.3669496E-03 0.3822613 at 30iterations 5.1348581E-04 8.5395813E-02 at 40iterations 1.5754069E-04 2.7515411E-02 at 50iterations finished qdiffx linear iterations at : 14:07:15 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.5754069E-04 2.7515411E-02 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 14:07:15 3.425u 0.172s 0:03.92 91.5% 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 14:07:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2415 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.988605 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): -6.993000 42.21400 ymin,ymax (A): 21.61200 75.31800 zmin,zma (A): 41.78300 84.72800 x,y,z range (A): 49.20700 53.70600 42.94500 scale (grids/A): 1.988605 object centre (A): 17.61050 48.46500 63.25550 number of atom coordinates read : 2415 total number of charged atoms : 2273 net assigned charge : 4.500021 assigned positive charge : 370.2409 centred at (gu) : 91.92152 92.56873 91.62978 assigned negative charge : -365.7415 centred at (gu) : 91.98981 92.91325 92.03389 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 75525 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21637 grid for indexing accessible points = 1.400000 m= 27761 mr = 51889 m= 4621 mr = 20192 m= 382 mr = 2775 m= 14 mr = 206 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 33241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 17963 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) : 0.6628682 object centre at (A) : 17.61050 48.46500 63.25550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5887634E-02 -7.5867637E-03 midg,1,midg; midg,igrid,midg 9.2702135E-03 -1.0238912E-02 1,midg,midg; igrid,midg,midg 3.5739735E-02 1.0826920E-02 gauss-seidel spectral radius is 0.9987295 estimated iterations to convergence 222 setup time was (sec) 0.6300000 now iterating at: 14:07:16 rms-change max change #iterations 4.481894 183.9217 at 10iterations 2.143759 76.17178 at 20iterations 1.032295 32.58186 at 30iterations 0.4944764 15.42625 at 40iterations 0.2383888 7.279481 at 50iterations 0.1149103 3.619152 at 60iterations 5.5279411E-02 1.733504 at 70iterations 2.6828904E-02 0.8230476 at 80iterations 1.3042206E-02 0.4037933 at 90iterations 6.4063845E-03 0.2082520 at 100iterations 3.2108393E-03 0.1001492 at 110iterations 1.6708155E-03 5.6087494E-02 at 120iterations finished qdiffx linear iterations at : 14:07:23 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 1.6708155E-03 5.6087494E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 14:07:24 7.953u 0.185s 0:08.45 96.2% 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 Sun Oct 9 2011 at 14:07:24 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 = 2415 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.982907 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): -6.993000 42.21400 ymin,ymax (A): 21.61200 75.31800 zmin,zma (A): 41.78300 84.72800 x,y,z range (A): 49.20700 53.70600 42.94500 scale (grids/A): 2.982907 object centre (A): 17.61050 48.46500 63.25550 number of atom coordinates read : 2415 total number of charged atoms : 2273 net assigned charge : 4.500021 assigned positive charge : 370.2409 centred at (gu) : 92.88204 93.85290 92.44440 assigned negative charge : -365.7415 centred at (gu) : 92.98456 94.36981 93.05093 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 174285 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21637 grid for indexing accessible points = 1.400000 m= 88740 mr = 125663 m= 32893 mr = 72000 m= 8401 mr = 26151 m= 1531 mr = 6146 m= 171 mr = 1075 m= 3 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9900000 number of dielectric boundary points 74884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 18182 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) : 1.988605 object centre at (A) : 17.61050 48.46500 63.25550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4451593 -0.1304868 midg,1,midg; midg,igrid,midg 0.2109678 -0.1813008 1,midg,midg; igrid,midg,midg 0.4345746 6.7126499E-03 gauss-seidel spectral radius is 0.9992770 estimated iterations to convergence 293 setup time was (sec) 1.230000 now iterating at: 14:07:25 rms-change max change #iterations 10.38779 424.3647 at 10iterations 6.111549 152.3193 at 20iterations 3.592479 78.10801 at 30iterations 2.101531 43.78930 at 40iterations 1.228597 24.51313 at 50iterations 0.7164358 12.59190 at 60iterations 0.4175026 7.959723 at 70iterations 0.2424503 4.050928 at 80iterations 0.1412081 2.429017 at 90iterations 8.2228124E-02 1.395180 at 100iterations 4.7851309E-02 0.9328558 at 110iterations 2.7999086E-02 0.5076332 at 120iterations 1.6483169E-02 0.2761459 at 130iterations 9.8712109E-03 0.1839447 at 140iterations 6.0775299E-03 0.1311646 at 150iterations 3.8836002E-03 8.5651398E-02 at 160iterations 2.6338177E-03 5.6777954E-02 at 170iterations 1.8986466E-03 4.1786194E-02 at 180iterations finished qdiffx linear iterations at : 14:07:37 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 1.8986466E-03 4.1786194E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 14:07:37 12.759u 0.201s 0:13.26 97.6% 0+0k 0+0io 0pf+0w