Mon Oct 10 14:38:51 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 Mon Oct 10 2011 at 14:38:51 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2449 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: 0.6255381 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): -7.483000 44.00500 ymin,ymax (A): 13.00300 69.91400 zmin,zma (A): 55.68000 107.4880 x,y,z range (A): 51.48800 56.91100 51.80800 scale (grids/A): 0.6255381 object centre (A): 18.26100 41.45850 81.58400 number of atom coordinates read : 2449 total number of charged atoms : 2290 net assigned charge : -3.999989 assigned positive charge : 359.1821 centred at (gu) : 89.86568 90.88406 89.91187 assigned negative charge : -363.1825 centred at (gu) : 89.62088 90.82982 89.88901 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6493 nv = 96 ne = 84 npr = 48931 no. pairs analyzed = 48931 no. exposed pairs = 3353 no. arc points = 23575 no. surface atoms = 1126 nbur = 1323 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 322 mr = 3302 m= 0 mr = 17 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2233 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7699 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5674358E-09 -2.0916140E-09 midg,1,midg; midg,igrid,midg -6.4214070E-09 2.1951584E-10 1,midg,midg; igrid,midg,midg -2.2809203E-08 1.3177920E-08 gauss-seidel spectral radius is 0.9867585 estimated iterations to convergence 71 setup time was (sec) 0.5900000 now iterating at: 14:38:52 rms-change max change #iterations 0.1249879 19.82005 at 10iterations 1.1547747E-02 1.783660 at 20iterations 1.0952876E-03 0.1712265 at 30iterations 1.0196117E-04 1.4732361E-02 at 40iterations 9.5855385E-06 1.4204979E-03 at 50iterations finished qdiffx linear iterations at : 14:38:55 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 9.5855385E-06 1.4204979E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 14:38:57 4.067u 0.270s 0:05.31 81.5% 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 Mon Oct 10 2011 at 14:38:57 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2449 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: 1.876614 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): -7.483000 44.00500 ymin,ymax (A): 13.00300 69.91400 zmin,zma (A): 55.68000 107.4880 x,y,z range (A): 51.48800 56.91100 51.80800 scale (grids/A): 1.876614 object centre (A): 18.26100 41.45850 81.58400 number of atom coordinates read : 2449 total number of charged atoms : 2290 net assigned charge : -3.999989 assigned positive charge : 359.1821 centred at (gu) : 89.59652 92.65161 89.73518 assigned negative charge : -363.1825 centred at (gu) : 88.86240 92.48914 89.66673 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 69877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23575 grid for indexing accessible points = 1.400000 m= 23290 mr = 46412 m= 3120 mr = 16153 m= 153 mr = 1552 m= 0 mr = 33 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 32290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 187 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 17998 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) : 0.6255381 object centre at (A) : 18.26100 41.45850 81.58400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9186368E-02 2.4921857E-03 midg,1,midg; midg,igrid,midg -5.8906977E-03 -5.7596518E-03 1,midg,midg; igrid,midg,midg -4.1392494E-02 8.1437267E-03 gauss-seidel spectral radius is 0.9985873 estimated iterations to convergence 211 setup time was (sec) 0.9300000 now iterating at: 14:38:58 rms-change max change #iterations 3.937813 204.2293 at 10iterations 1.821628 68.25861 at 20iterations 0.8373703 31.30659 at 30iterations 0.3869775 12.27668 at 40iterations 0.1779221 6.454896 at 50iterations 8.2040906E-02 3.019671 at 60iterations 3.7713572E-02 1.248587 at 70iterations 1.7505417E-02 0.6926298 at 80iterations 8.0385497E-03 0.2392764 at 90iterations 3.7191662E-03 0.1324291 at 100iterations 1.7185210E-03 5.8234572E-02 at 110iterations 7.9188024E-04 2.9372096E-02 at 120iterations finished qdiffx linear iterations at : 14:39:06 total time elapsed so far: 9.260000 # loops : 120 mean,max change (kT/e) : 7.9188024E-04 2.9372096E-02 energy calculations done at 9.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.440000 DelPhi exited at 14:39:07 9.440u 0.312s 0:10.29 94.7% 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 Mon Oct 10 2011 at 14:39:07 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2449 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: 2.814921 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): -7.483000 44.00500 ymin,ymax (A): 13.00300 69.91400 zmin,zma (A): 55.68000 107.4880 x,y,z range (A): 51.48800 56.91100 51.80800 scale (grids/A): 2.814921 object centre (A): 18.26100 41.45850 81.58400 number of atom coordinates read : 2449 total number of charged atoms : 2290 net assigned charge : -3.999989 assigned positive charge : 359.1821 centred at (gu) : 89.39483 93.97726 89.60271 assigned negative charge : -363.1825 centred at (gu) : 88.29342 93.73368 89.49990 start vw surface at 0.1600000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 161541 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23575 grid for indexing accessible points = 1.400000 m= 77314 mr = 113267 m= 25531 mr = 61237 m= 5095 mr = 19196 m= 570 mr = 3331 m= 31 mr = 269 m= 0 mr = 14 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.590000 number of dielectric boundary points 72768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 18320 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) : 1.876614 object centre at (A) : 18.26100 41.45850 81.58400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3160610 3.6904294E-02 midg,1,midg; midg,igrid,midg -6.4407967E-02 -0.1068307 1,midg,midg; igrid,midg,midg -0.4309011 3.0387955E-02 gauss-seidel spectral radius is 0.9992524 estimated iterations to convergence 289 setup time was (sec) 1.910000 now iterating at: 14:39:09 rms-change max change #iterations 9.484047 383.3860 at 10iterations 5.595683 130.8619 at 20iterations 3.259527 75.64849 at 30iterations 1.892829 40.23488 at 40iterations 1.094899 23.95621 at 50iterations 0.6335034 12.96672 at 60iterations 0.3644273 7.807344 at 70iterations 0.2100633 4.141244 at 80iterations 0.1203376 2.340050 at 90iterations 6.9415674E-02 1.448235 at 100iterations 3.9744269E-02 0.7724762 at 110iterations 2.2852706E-02 0.4441223 at 120iterations 1.3107336E-02 0.3157310 at 130iterations 7.5185634E-03 0.1413460 at 140iterations 4.3007033E-03 8.4396362E-02 at 150iterations 2.4630867E-03 4.7309875E-02 at 160iterations 1.4149119E-03 2.4979115E-02 at 170iterations 8.0897089E-04 1.6410351E-02 at 180iterations finished qdiffx linear iterations at : 14:39:23 total time elapsed so far: 15.61000 # loops : 180 mean,max change (kT/e) : 8.0897089E-04 1.6410351E-02 energy calculations done at 15.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.78000 DelPhi exited at 14:39:24 15.779u 0.334s 0:16.63 96.8% 0+0k 0+0io 0pf+0w