Tue Oct 11 03:24:02 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 Tue Oct 11 2011 at 03:24:03 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1184 !!! WARNING: HIT 60 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7205895 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): -6.908000 31.91200 ymin,ymax (A): 1.116000 39.54100 zmin,zma (A): -3.252000 46.15200 x,y,z range (A): 38.82000 38.42500 49.40400 scale (grids/A): 0.7205895 object centre (A): 12.50200 20.32850 21.45000 number of atom coordinates read : 1184 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 177.3651 centred at (gu) : 88.79482 89.40998 89.03083 assigned negative charge : -171.8512 centred at (gu) : 88.47900 89.38202 89.06127 start vw surface at 5.0000001E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 4168 nv = 96 ne = 84 npr = 23409 no. pairs analyzed = 23409 no. exposed pairs = 1495 no. arc points = 10973 no. surface atoms = 504 nbur = 680 mkacc time = 4.0000003E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 235 mr = 2126 m= 0 mr = 40 time to grow re-entrant surface = 5.0000001E-02 no. cavity mid-points inaccessible to solvent = 46 time to turn everything in is 0.1100000 number of dielectric boundary points 2237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 941 ## 87 charges are in solution ## iepsmp to db, and charging done at 0.1700000 number of grid points assigned charge 4328 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0766136E-08 4.4973394E-08 midg,1,midg; midg,igrid,midg 6.0759298E-08 6.7008571E-08 1,midg,midg; igrid,midg,midg -6.8889911E-08 1.3952345E-07 gauss-seidel spectral radius is 0.9898741 estimated iterations to convergence 81 setup time was (sec) 0.2800000 now iterating at: 03:24:03 rms-change max change #iterations 0.1594032 31.04485 at 10iterations 2.0540660E-02 3.579521 at 20iterations 2.5241962E-03 0.4672432 at 30iterations 3.2373529E-04 6.0691833E-02 at 40iterations 3.9830818E-05 7.9383850E-03 at 50iterations finished qdiffx linear iterations at : 03:24:06 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 3.9830818E-05 7.9383850E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 03:24:06 3.249u 0.183s 0:03.87 88.3% 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 Tue Oct 11 2011 at 03:24:07 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1184 !!! WARNING: HIT 60 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.161768 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): -6.908000 31.91200 ymin,ymax (A): 1.116000 39.54100 zmin,zma (A): -3.252000 46.15200 x,y,z range (A): 38.82000 38.42500 49.40400 scale (grids/A): 2.161768 object centre (A): 12.50200 20.32850 21.45000 number of atom coordinates read : 1184 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 177.3651 centred at (gu) : 86.38452 88.22998 87.09258 assigned negative charge : -171.8512 centred at (gu) : 85.43708 88.14635 87.18398 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 43574 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10973 grid for indexing accessible points = 1.400000 m= 16067 mr = 28484 m= 3028 mr = 11926 m= 289 mr = 1995 m= 16 mr = 162 m= 0 mr = 12 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 1348 time to turn everything in is 0.2400000 number of dielectric boundary points 20395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8433 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) : 0.7205895 object centre at (A) : 12.50200 20.32850 21.45000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6542768E-03 2.7020560E-03 midg,1,midg; midg,igrid,midg 2.8650332E-02 2.6862886E-02 1,midg,midg; igrid,midg,midg -2.7164549E-02 3.5081688E-02 gauss-seidel spectral radius is 0.9987811 estimated iterations to convergence 227 setup time was (sec) 0.4500000 now iterating at: 03:24:07 rms-change max change #iterations 3.517195 194.4061 at 10iterations 1.722865 82.59310 at 20iterations 0.8330050 32.58247 at 30iterations 0.4063235 16.56446 at 40iterations 0.1985253 8.224064 at 50iterations 9.6322224E-02 4.071404 at 60iterations 4.6879582E-02 1.792090 at 70iterations 2.2846535E-02 1.020369 at 80iterations 1.1105475E-02 0.4310389 at 90iterations 5.4245736E-03 0.1994820 at 100iterations 2.6439202E-03 0.1126404 at 110iterations 1.2913174E-03 4.9549103E-02 at 120iterations finished qdiffx linear iterations at : 03:24:14 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 1.2913174E-03 4.9549103E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 03:24:15 7.489u 0.193s 0:08.07 95.0% 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 Tue Oct 11 2011 at 03:24:15 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1184 !!! WARNING: HIT 60 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.242652 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): -6.908000 31.91200 ymin,ymax (A): 1.116000 39.54100 zmin,zma (A): -3.252000 46.15200 x,y,z range (A): 38.82000 38.42500 49.40400 scale (grids/A): 3.242652 object centre (A): 12.50200 20.32850 21.45000 number of atom coordinates read : 1184 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 177.3651 centred at (gu) : 84.57682 87.34499 85.63896 assigned negative charge : -171.8512 centred at (gu) : 83.15563 87.21959 85.77604 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 100265 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10973 grid for indexing accessible points = 1.400000 m= 50066 mr = 68740 m= 20027 mr = 40781 m= 5696 mr = 16400 m= 1164 mr = 4487 m= 152 mr = 879 m= 12 mr = 108 m= 0 mr = 12 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 4570 time to turn everything in is 0.6700000 number of dielectric boundary points 45975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 8488 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) : 2.161768 object centre at (A) : 12.50200 20.32850 21.45000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5795353E-02 1.2735807E-02 midg,1,midg; midg,igrid,midg 0.2593482 0.2295047 1,midg,midg; igrid,midg,midg -0.2411305 0.2677878 gauss-seidel spectral radius is 0.9992760 estimated iterations to convergence 293 setup time was (sec) 0.9000000 now iterating at: 03:24:16 rms-change max change #iterations 7.709991 269.0648 at 10iterations 4.448279 109.1833 at 20iterations 2.559708 57.02253 at 30iterations 1.474630 33.44455 at 40iterations 0.8475221 19.56419 at 50iterations 0.4878717 10.47090 at 60iterations 0.2812810 6.190894 at 70iterations 0.1617776 3.541571 at 80iterations 9.3049631E-02 1.858877 at 90iterations 5.3591140E-02 1.167370 at 100iterations 3.0921912E-02 0.6910877 at 110iterations 1.7778251E-02 0.4220128 at 120iterations 1.0259275E-02 0.2241459 at 130iterations 5.8941748E-03 0.1282730 at 140iterations 3.4041200E-03 7.1790695E-02 at 150iterations 1.9608962E-03 4.9651265E-02 at 160iterations 1.1255987E-03 2.7841091E-02 at 170iterations 6.5119268E-04 1.3755798E-02 at 180iterations finished qdiffx linear iterations at : 03:24:27 total time elapsed so far: 11.65000 # loops : 180 mean,max change (kT/e) : 6.5119268E-04 1.3755798E-02 energy calculations done at 11.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 03:24:27 11.789u 0.190s 0:12.26 97.6% 0+0k 0+0io 0pf+0w