Sun Oct 9 22:07:59 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+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 Sun Oct 9 2011 at 22:07:59 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2526 !!! WARNING: SEP 142 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: 0.6568629 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): -11.77300 38.17900 ymin,ymax (A): -22.24400 31.95300 zmin,zma (A): -11.17200 41.30700 x,y,z range (A): 49.95200 54.19700 52.47900 scale (grids/A): 0.6568629 object centre (A): 13.20300 4.854501 15.06750 number of atom coordinates read : 2526 total number of charged atoms : 2402 net assigned charge : 6.525012 assigned positive charge : 385.8950 centred at (gu) : 90.77468 89.59638 90.06932 assigned negative charge : -379.3706 centred at (gu) : 90.67588 89.43602 90.05817 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7233 nv = 96 ne = 84 npr = 50523 no. pairs analyzed = 50523 no. exposed pairs = 3091 no. arc points = 22063 no. surface atoms = 1051 nbur = 1475 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 399 mr = 3913 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.2100000 number of dielectric boundary points 3668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2199 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8646 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3062747E-08 1.7465100E-08 midg,1,midg; midg,igrid,midg -1.5194944E-08 3.9854946E-08 1,midg,midg; igrid,midg,midg -2.0639415E-09 3.8408036E-08 gauss-seidel spectral radius is 0.9879826 estimated iterations to convergence 74 setup time was (sec) 0.4000000 now iterating at: 22:08:00 rms-change max change #iterations 0.1574423 23.69048 at 10iterations 1.6426990E-02 2.249779 at 20iterations 1.7407419E-03 0.2517996 at 30iterations 1.8242144E-04 2.7736664E-02 at 40iterations 1.9138359E-05 2.3698807E-03 at 50iterations finished qdiffx linear iterations at : 22:08:03 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.9138359E-05 2.3698807E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 22:08:03 3.420u 0.158s 0:03.87 92.2% 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 22:08:03 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2526 !!! WARNING: SEP 142 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.970589 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): -11.77300 38.17900 ymin,ymax (A): -22.24400 31.95300 zmin,zma (A): -11.17200 41.30700 x,y,z range (A): 49.95200 54.19700 52.47900 scale (grids/A): 1.970589 object centre (A): 13.20300 4.854501 15.06750 number of atom coordinates read : 2526 total number of charged atoms : 2402 net assigned charge : 6.525012 assigned positive charge : 385.8950 centred at (gu) : 92.32368 88.78873 90.20748 assigned negative charge : -379.3706 centred at (gu) : 92.02767 88.30786 90.17445 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 77920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22063 grid for indexing accessible points = 1.400000 m= 27227 mr = 53342 m= 4587 mr = 20074 m= 327 mr = 2899 m= 5 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1488 time to turn everything in is 0.3900000 number of dielectric boundary points 33586 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 18971 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) : 0.6568629 object centre at (A) : 13.20300 4.854501 15.06750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0742661E-02 -6.6851615E-03 midg,1,midg; midg,igrid,midg 2.0875337E-02 5.1664460E-02 1,midg,midg; igrid,midg,midg -1.6295891E-02 1.9893831E-02 gauss-seidel spectral radius is 0.9987124 estimated iterations to convergence 221 setup time was (sec) 0.6000000 now iterating at: 22:08:04 rms-change max change #iterations 4.449601 170.2827 at 10iterations 2.123106 75.36211 at 20iterations 1.016345 32.72573 at 30iterations 0.4853652 14.76236 at 40iterations 0.2318905 6.848746 at 50iterations 0.1109600 3.209904 at 60iterations 5.2957572E-02 1.751285 at 70iterations 2.5262086E-02 0.7790394 at 80iterations 1.2109203E-02 0.3809547 at 90iterations 5.8056735E-03 0.1912301 at 100iterations 2.7630467E-03 8.7468624E-02 at 110iterations 1.3253347E-03 4.0871620E-02 at 120iterations finished qdiffx linear iterations at : 22:08:11 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 1.3253347E-03 4.0871620E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 22:08:12 7.908u 0.212s 0:08.45 95.9% 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 22:08:12 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2526 !!! WARNING: SEP 142 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.955883 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): -11.77300 38.17900 ymin,ymax (A): -22.24400 31.95300 zmin,zma (A): -11.17200 41.30700 x,y,z range (A): 49.95200 54.19700 52.47900 scale (grids/A): 2.955883 object centre (A): 13.20300 4.854501 15.06750 number of atom coordinates read : 2526 total number of charged atoms : 2402 net assigned charge : 6.525012 assigned positive charge : 385.8950 centred at (gu) : 93.48543 88.18305 90.31100 assigned negative charge : -379.3706 centred at (gu) : 93.04147 87.46172 90.26167 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 180240 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22063 grid for indexing accessible points = 1.400000 m= 88850 mr = 129664 m= 31757 mr = 72528 m= 8225 mr = 25293 m= 1482 mr = 6307 m= 137 mr = 1106 m= 2 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 4726 time to turn everything in is 1.010000 number of dielectric boundary points 75718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 19211 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) : 1.970589 object centre at (A) : 13.20300 4.854501 15.06750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2028857 -0.2722212 midg,1,midg; midg,igrid,midg 7.9000056E-02 0.4564387 1,midg,midg; igrid,midg,midg -0.2693336 0.2398381 gauss-seidel spectral radius is 0.9992800 estimated iterations to convergence 294 setup time was (sec) 1.250000 now iterating at: 22:08:13 rms-change max change #iterations 10.29180 430.1606 at 10iterations 5.991814 123.0059 at 20iterations 3.477959 75.20585 at 30iterations 2.019699 42.65649 at 40iterations 1.170537 21.91316 at 50iterations 0.6791385 13.82881 at 60iterations 0.3928914 6.960358 at 70iterations 0.2275082 4.179367 at 80iterations 0.1318078 2.270535 at 90iterations 7.6168731E-02 1.399550 at 100iterations 4.4019718E-02 0.7617171 at 110iterations 2.5471117E-02 0.4350214 at 120iterations 1.4751851E-02 0.2492785 at 130iterations 8.5232053E-03 0.1690598 at 140iterations 4.9289698E-03 8.4319115E-02 at 150iterations 2.8523246E-03 5.5183411E-02 at 160iterations 1.6494533E-03 2.7990341E-02 at 170iterations 9.5459615E-04 1.8002510E-02 at 180iterations finished qdiffx linear iterations at : 22:08:25 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 9.5459615E-04 1.8002510E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 22:08:25 12.967u 0.206s 0:13.63 96.5% 0+0k 0+0io 0pf+0w