Sat Oct 8 15:45:59 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 8 2011 at 15:45:59 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 = 2274 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: 0.6464148 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): -17.84900 30.71000 ymin,ymax (A): 4.324000 49.87700 zmin,zma (A): -18.76400 36.30900 x,y,z range (A): 48.55900 45.55300 55.07300 scale (grids/A): 0.6464148 object centre (A): 6.430500 27.10050 8.772499 number of atom coordinates read : 2274 total number of charged atoms : 2213 net assigned charge : 4.000005 assigned positive charge : 338.9113 centred at (gu) : 89.05151 91.06453 90.22645 assigned negative charge : -334.9118 centred at (gu) : 89.03954 90.97239 90.26072 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6517 nv = 96 ne = 84 npr = 45132 no. pairs analyzed = 45132 no. exposed pairs = 2891 no. arc points = 19937 no. surface atoms = 983 nbur = 1291 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3613 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2600000 number of dielectric boundary points 3258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1928 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7773 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0449759E-08 2.8845590E-09 midg,1,midg; midg,igrid,midg -3.3057033E-09 2.2301389E-08 1,midg,midg; igrid,midg,midg 6.5936043E-09 6.8353776E-09 gauss-seidel spectral radius is 0.9875741 estimated iterations to convergence 73 setup time was (sec) 0.4700000 now iterating at: 15:46:00 rms-change max change #iterations 0.1384823 19.81592 at 10iterations 1.4210417E-02 2.035769 at 20iterations 1.4586719E-03 0.2301979 at 30iterations 1.5895885E-04 2.5613785E-02 at 40iterations 2.1771235E-05 3.0899048E-03 at 50iterations finished qdiffx linear iterations at : 15:46:02 total time elapsed so far: 2.850000 # loops : 50 mean,max change (kT/e) : 2.1771235E-05 3.0899048E-03 energy calculations done at 2.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.010000 DelPhi exited at 15:46:03 3.017u 0.162s 0:03.45 91.8% 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 Sat Oct 8 2011 at 15:46:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2274 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: 1.939244 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): -17.84900 30.71000 ymin,ymax (A): 4.324000 49.87700 zmin,zma (A): -18.76400 36.30900 x,y,z range (A): 48.55900 45.55300 55.07300 scale (grids/A): 1.939244 object centre (A): 6.430500 27.10050 8.772499 number of atom coordinates read : 2274 total number of charged atoms : 2213 net assigned charge : 4.000005 assigned positive charge : 338.9113 centred at (gu) : 87.15398 93.19315 90.67905 assigned negative charge : -334.9118 centred at (gu) : 87.11851 92.91720 90.78226 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19937 grid for indexing accessible points = 1.400000 m= 26428 mr = 48559 m= 4814 mr = 19661 m= 285 mr = 3217 m= 8 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 419 time to turn everything in is 0.5000000 number of dielectric boundary points 29914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 17452 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) : 0.6464148 object centre at (A) : 6.430500 27.10050 8.772499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3420829E-02 5.6127864E-03 midg,1,midg; midg,igrid,midg -1.5347864E-03 2.1867713E-02 1,midg,midg; igrid,midg,midg -4.4199493E-02 1.6795526E-03 gauss-seidel spectral radius is 0.9986525 estimated iterations to convergence 216 setup time was (sec) 0.7600000 now iterating at: 15:46:04 rms-change max change #iterations 4.074665 170.8475 at 10iterations 1.912348 79.12222 at 20iterations 0.9009672 30.82687 at 30iterations 0.4248829 14.95431 at 40iterations 0.2000463 6.894445 at 50iterations 9.4427690E-02 3.153872 at 60iterations 4.4543620E-02 1.466336 at 70iterations 2.0919878E-02 0.6698427 at 80iterations 9.8226285E-03 0.3373212 at 90iterations 4.6540014E-03 0.1372662 at 100iterations 2.1979935E-03 7.3531151E-02 at 110iterations 1.0345385E-03 3.0598164E-02 at 120iterations finished qdiffx linear iterations at : 15:46:10 total time elapsed so far: 6.650000 # loops : 120 mean,max change (kT/e) : 1.0345385E-03 3.0598164E-02 energy calculations done at 6.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.820000 DelPhi exited at 15:46:10 6.821u 0.172s 0:07.30 95.7% 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 Sat Oct 8 2011 at 15:46:10 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 = 2274 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: 2.908866 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): -17.84900 30.71000 ymin,ymax (A): 4.324000 49.87700 zmin,zma (A): -18.76400 36.30900 x,y,z range (A): 48.55900 45.55300 55.07300 scale (grids/A): 2.908866 object centre (A): 6.430500 27.10050 8.772499 number of atom coordinates read : 2274 total number of charged atoms : 2213 net assigned charge : 4.000005 assigned positive charge : 338.9113 centred at (gu) : 85.73100 94.78947 91.01852 assigned negative charge : -334.9118 centred at (gu) : 85.67773 94.37571 91.17338 start vw surface at 0.1200000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 161651 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19937 grid for indexing accessible points = 1.400000 m= 83323 mr = 117682 m= 32627 mr = 68470 m= 9032 mr = 26519 m= 1356 mr = 7026 m= 75 mr = 905 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 1469 time to turn everything in is 1.230000 number of dielectric boundary points 67444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 17703 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) : 1.939244 object centre at (A) : 6.430500 27.10050 8.772499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2729039 6.2386863E-02 midg,1,midg; midg,igrid,midg -4.7824357E-02 0.1610319 1,midg,midg; igrid,midg,midg -0.6113998 -6.4136973E-03 gauss-seidel spectral radius is 0.9992622 estimated iterations to convergence 291 setup time was (sec) 1.490000 now iterating at: 15:46:12 rms-change max change #iterations 9.532044 366.4122 at 10iterations 5.599601 122.5376 at 20iterations 3.273143 81.17805 at 30iterations 1.908672 38.46694 at 40iterations 1.111298 26.14330 at 50iterations 0.6447025 11.91798 at 60iterations 0.3739027 7.130725 at 70iterations 0.2160266 3.884756 at 80iterations 0.1248784 2.339602 at 90iterations 7.2139010E-02 1.316504 at 100iterations 4.1638598E-02 0.7494583 at 110iterations 2.3914594E-02 0.4297304 at 120iterations 1.3801782E-02 0.3007278 at 130iterations 7.9446575E-03 0.1420250 at 140iterations 4.5764055E-03 8.4292322E-02 at 150iterations 2.6386313E-03 4.6104431E-02 at 160iterations 1.5161047E-03 2.8890610E-02 at 170iterations 8.7332429E-04 1.7172813E-02 at 180iterations finished qdiffx linear iterations at : 15:46:21 total time elapsed so far: 10.84000 # loops : 180 mean,max change (kT/e) : 8.7332429E-04 1.7172813E-02 energy calculations done at 10.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.02000 DelPhi exited at 15:46:22 11.021u 0.194s 0:11.51 97.3% 0+0k 0+0io 0pf+0w