Mon Oct 10 16:26:56 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+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 Mon Oct 10 2011 at 16:26:56 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 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: 0.5737032 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): 60.47500 112.3620 ymin,ymax (A): 224.9630 287.0160 zmin,zma (A): 79.21200 127.3290 x,y,z range (A): 51.88700 62.05299 48.11700 scale (grids/A): 0.5737032 object centre (A): 86.41850 255.9895 103.2705 number of atom coordinates read : 2579 total number of charged atoms : 2436 net assigned charge : 7.000030 assigned positive charge : 391.7644 centred at (gu) : 90.53283 89.83328 91.79109 assigned negative charge : -384.7653 centred at (gu) : 90.40213 89.67548 91.90785 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5485 nv = 96 ne = 84 npr = 50367 no. pairs analyzed = 50367 no. exposed pairs = 3555 no. arc points = 25427 no. surface atoms = 1174 nbur = 1405 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 278 mr = 2637 m= 0 mr = 22 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3104 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2519 ## 344 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7067 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9904209E-09 -9.1501817E-10 midg,1,midg; midg,igrid,midg -1.2692128E-09 3.4930556E-09 1,midg,midg; igrid,midg,midg -6.8440559E-10 3.6662795E-09 gauss-seidel spectral radius is 0.9842935 estimated iterations to convergence 66 setup time was (sec) 0.6400000 now iterating at: 16:26:57 rms-change max change #iterations 8.7248281E-02 14.68735 at 10iterations 6.6484464E-03 1.055382 at 20iterations 4.9206929E-04 7.7766418E-02 at 30iterations 3.8204595E-05 6.4773560E-03 at 40iterations 2.8822303E-06 5.0759315E-04 at 50iterations finished qdiffx linear iterations at : 16:27:00 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 2.8822303E-06 5.0759315E-04 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 16:27:01 4.176u 0.243s 0:04.93 89.4% 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 Mon Oct 10 2011 at 16:27:01 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 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: 1.721110 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): 60.47500 112.3620 ymin,ymax (A): 224.9630 287.0160 zmin,zma (A): 79.21200 127.3290 x,y,z range (A): 51.88700 62.05299 48.11700 scale (grids/A): 1.721110 object centre (A): 86.41850 255.9895 103.2705 number of atom coordinates read : 2579 total number of charged atoms : 2436 net assigned charge : 7.000030 assigned positive charge : 391.7644 centred at (gu) : 91.59753 89.49907 95.37268 assigned negative charge : -384.7653 centred at (gu) : 91.20593 89.02622 95.72310 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 59196 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25427 grid for indexing accessible points = 1.400000 m= 19441 mr = 37640 m= 2690 mr = 13443 m= 84 mr = 1502 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 123 time to turn everything in is 0.5600000 number of dielectric boundary points 28814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 248 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 18864 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) : 0.5737032 object centre at (A) : 86.41850 255.9895 103.2705 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9690440E-03 -1.0990410E-02 midg,1,midg; midg,igrid,midg 2.6053279E-03 6.8502324E-03 1,midg,midg; igrid,midg,midg 4.6597514E-03 1.5895553E-02 gauss-seidel spectral radius is 0.9983336 estimated iterations to convergence 194 setup time was (sec) 0.8700000 now iterating at: 16:27:02 rms-change max change #iterations 3.442995 158.9831 at 10iterations 1.484482 66.04633 at 20iterations 0.6408842 23.58486 at 30iterations 0.2762530 10.64038 at 40iterations 0.1191878 4.107437 at 50iterations 5.1558398E-02 1.791603 at 60iterations 2.2359524E-02 0.8154507 at 70iterations 9.6550668E-03 0.3579903 at 80iterations 4.1824980E-03 0.1970456 at 90iterations 1.8031629E-03 6.7306519E-02 at 100iterations 7.8417617E-04 3.1157669E-02 at 110iterations 3.3870724E-04 1.2080193E-02 at 120iterations finished qdiffx linear iterations at : 16:27:11 total time elapsed so far: 9.230000 # loops : 120 mean,max change (kT/e) : 3.3870724E-04 1.2080193E-02 energy calculations done at 9.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.420000 DelPhi exited at 16:27:11 9.425u 0.299s 0:10.24 94.8% 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 Mon Oct 10 2011 at 16:27:11 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 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: 2.581664 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): 60.47500 112.3620 ymin,ymax (A): 224.9630 287.0160 zmin,zma (A): 79.21200 127.3290 x,y,z range (A): 51.88700 62.05299 48.11700 scale (grids/A): 2.581664 object centre (A): 86.41850 255.9895 103.2705 number of atom coordinates read : 2579 total number of charged atoms : 2436 net assigned charge : 7.000030 assigned positive charge : 391.7644 centred at (gu) : 92.39629 89.24834 98.05873 assigned negative charge : -384.7653 centred at (gu) : 91.80892 88.53925 98.58456 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 136951 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25427 grid for indexing accessible points = 1.400000 m= 63116 mr = 92365 m= 21800 mr = 49049 m= 4403 mr = 16938 m= 410 mr = 3084 m= 9 mr = 201 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 404 time to turn everything in is 1.370000 number of dielectric boundary points 65052 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 19473 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) : 1.721110 object centre at (A) : 86.41850 255.9895 103.2705 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0830425E-02 -0.1580252 midg,1,midg; midg,igrid,midg 3.4450952E-02 -0.3870064 1,midg,midg; igrid,midg,midg 4.9176916E-02 0.1508931 gauss-seidel spectral radius is 0.9991762 estimated iterations to convergence 275 setup time was (sec) 1.700000 now iterating at: 16:27:13 rms-change max change #iterations 8.703699 284.2952 at 10iterations 4.937157 136.4742 at 20iterations 2.768848 60.98475 at 30iterations 1.552180 37.21845 at 40iterations 0.8667748 20.18973 at 50iterations 0.4842388 10.98395 at 60iterations 0.2700293 6.208600 at 70iterations 0.1500949 3.293812 at 80iterations 8.3552726E-02 1.722092 at 90iterations 4.6557438E-02 1.048325 at 100iterations 2.5884893E-02 0.5199518 at 110iterations 1.4382021E-02 0.3199852 at 120iterations 8.0120582E-03 0.1678495 at 130iterations 4.4518574E-03 9.7733498E-02 at 140iterations 2.4731357E-03 5.2285194E-02 at 150iterations 1.3773633E-03 3.0883789E-02 at 160iterations 7.6506194E-04 1.6380310E-02 at 170iterations 4.2646076E-04 9.1190636E-03 at 180iterations finished qdiffx linear iterations at : 16:27:27 total time elapsed so far: 15.50000 # loops : 180 mean,max change (kT/e) : 4.2646076E-04 9.1190636E-03 energy calculations done at 15.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.69000 DelPhi exited at 16:27:28 15.688u 0.322s 0:16.43 97.3% 0+0k 0+0io 0pf+0w