Sat Oct 8 12:50:06 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 Sat Oct 8 2011 at 12:50:06 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2240 !!! WARNING: SEP 175 has a net charge of -0.4750 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: 0.6055863 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): -6.902000 51.88400 ymin,ymax (A): -14.95100 34.22400 zmin,zma (A): -14.43100 29.88000 x,y,z range (A): 58.78600 49.17500 44.31100 scale (grids/A): 0.6055863 object centre (A): 22.49100 9.636499 7.724500 number of atom coordinates read : 2240 total number of charged atoms : 2103 net assigned charge : -3.974980 assigned positive charge : 303.4129 centred at (gu) : 89.98381 88.73497 89.98834 assigned negative charge : -307.3884 centred at (gu) : 89.73689 88.80948 89.94404 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5753 nv = 96 ne = 84 npr = 46437 no. pairs analyzed = 46437 no. exposed pairs = 3027 no. arc points = 21393 no. surface atoms = 1034 nbur = 1206 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 289 mr = 2859 m= 0 mr = 27 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1973 ## 137 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6865 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5937329E-09 -5.4635035E-10 midg,1,midg; midg,igrid,midg 6.7517486E-10 -3.4967864E-09 1,midg,midg; igrid,midg,midg -1.0805136E-08 6.1462115E-09 gauss-seidel spectral radius is 0.9858700 estimated iterations to convergence 69 setup time was (sec) 0.3900000 now iterating at: 12:50:07 rms-change max change #iterations 0.1036156 18.52379 at 10iterations 9.9398158E-03 1.746819 at 20iterations 1.8076415E-03 0.3764343 at 30iterations 6.0295372E-04 0.1342087 at 40iterations 2.1929217E-04 4.8732758E-02 at 50iterations finished qdiffx linear iterations at : 12:50:10 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 2.1929217E-04 4.8732758E-02 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 12:50:10 3.632u 0.212s 0:04.16 92.3% 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 12:50:10 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2240 !!! WARNING: SEP 175 has a net charge of -0.4750 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: 1.816759 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): -6.902000 51.88400 ymin,ymax (A): -14.95100 34.22400 zmin,zma (A): -14.43100 29.88000 x,y,z range (A): 58.78600 49.17500 44.31100 scale (grids/A): 1.816759 object centre (A): 22.49100 9.636499 7.724500 number of atom coordinates read : 2240 total number of charged atoms : 2103 net assigned charge : -3.974980 assigned positive charge : 303.4129 centred at (gu) : 89.95129 86.20483 89.96504 assigned negative charge : -307.3884 centred at (gu) : 89.21088 86.42856 89.83241 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 62752 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21393 grid for indexing accessible points = 1.400000 m= 20372 mr = 41563 m= 2965 mr = 13692 m= 138 mr = 1555 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 29371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 16495 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) : 0.6055863 object centre at (A) : 22.49100 9.636499 7.724500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5340206E-03 -5.7885968E-03 midg,1,midg; midg,igrid,midg -2.3263297E-03 -5.2287891E-03 1,midg,midg; igrid,midg,midg -3.6377199E-02 2.3985589E-02 gauss-seidel spectral radius is 0.9984807 estimated iterations to convergence 203 setup time was (sec) 0.5600000 now iterating at: 12:50:11 rms-change max change #iterations 3.412887 189.9931 at 10iterations 1.524688 64.95889 at 20iterations 0.6849098 29.27905 at 30iterations 0.3060297 11.27704 at 40iterations 0.1380550 4.598455 at 50iterations 6.2188163E-02 2.130516 at 60iterations 2.8170997E-02 1.279388 at 70iterations 1.2984673E-02 0.4486525 at 80iterations 6.1809891E-03 0.2381897 at 90iterations 3.1587488E-03 0.1620941 at 100iterations 1.7614665E-03 7.6408386E-02 at 110iterations 1.0985930E-03 5.0178528E-02 at 120iterations finished qdiffx linear iterations at : 12:50:19 total time elapsed so far: 8.160000 # loops : 120 mean,max change (kT/e) : 1.0985930E-03 5.0178528E-02 energy calculations done at 8.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 12:50:19 8.291u 0.231s 0:08.86 96.1% 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 12:50:19 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2240 !!! WARNING: SEP 175 has a net charge of -0.4750 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: 2.725138 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): -6.902000 51.88400 ymin,ymax (A): -14.95100 34.22400 zmin,zma (A): -14.43100 29.88000 x,y,z range (A): 58.78600 49.17500 44.31100 scale (grids/A): 2.725138 object centre (A): 22.49100 9.636499 7.724500 number of atom coordinates read : 2240 total number of charged atoms : 2103 net assigned charge : -3.974980 assigned positive charge : 303.4129 centred at (gu) : 89.92696 84.30736 89.94754 assigned negative charge : -307.3884 centred at (gu) : 88.81645 84.64286 89.74868 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 145455 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21393 grid for indexing accessible points = 1.400000 m= 67174 mr = 101869 m= 22698 mr = 52227 m= 5106 mr = 17007 m= 643 mr = 3420 m= 29 mr = 394 m= 0 mr = 11 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8300000 number of dielectric boundary points 66177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 16822 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) : 1.816759 object centre at (A) : 22.49100 9.636499 7.724500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7444361E-02 -4.5739006E-02 midg,1,midg; midg,igrid,midg -4.5821883E-02 -3.8443100E-02 1,midg,midg; igrid,midg,midg -0.4868055 0.4480610 gauss-seidel spectral radius is 0.9992152 estimated iterations to convergence 282 setup time was (sec) 1.090000 now iterating at: 12:50:20 rms-change max change #iterations 8.208062 323.9821 at 10iterations 4.740361 122.6064 at 20iterations 2.708629 64.42140 at 30iterations 1.546434 37.37305 at 40iterations 0.8775017 19.05376 at 50iterations 0.4976413 10.09298 at 60iterations 0.2831230 5.742184 at 70iterations 0.1603858 3.614713 at 80iterations 9.0951309E-02 1.829748 at 90iterations 5.1501866E-02 1.177616 at 100iterations 2.9111471E-02 0.6636500 at 110iterations 1.6531350E-02 0.3405080 at 120iterations 9.3923882E-03 0.1876411 at 130iterations 5.3775241E-03 0.1137009 at 140iterations 3.1234247E-03 6.5742493E-02 at 150iterations 1.8492407E-03 4.0939331E-02 at 160iterations 1.1540696E-03 2.9994965E-02 at 170iterations 7.6253596E-04 2.0233154E-02 at 180iterations finished qdiffx linear iterations at : 12:50:33 total time elapsed so far: 13.47000 # loops : 180 mean,max change (kT/e) : 7.6253596E-04 2.0233154E-02 energy calculations done at 13.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.60000 DelPhi exited at 12:50:33 13.600u 0.252s 0:14.14 97.9% 0+0k 0+0io 0pf+0w