Tue Oct 11 03:45:05 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 Tue Oct 11 2011 at 03:45:05 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2794 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6408294 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): -10.61200 36.61900 ymin,ymax (A): -26.45600 23.38700 zmin,zma (A): -10.32600 45.22700 x,y,z range (A): 47.23100 49.84300 55.55300 scale (grids/A): 0.6408294 object centre (A): 13.00350 -1.534500 17.45050 number of atom coordinates read : 2794 total number of charged atoms : 2641 net assigned charge : 2.162019 assigned positive charge : 423.4436 centred at (gu) : 90.05730 89.89092 91.79287 assigned negative charge : -421.2823 centred at (gu) : 89.82320 89.78311 91.76293 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7421 nv = 96 ne = 84 npr = 57917 no. pairs analyzed = 57917 no. exposed pairs = 3290 no. arc points = 22617 no. surface atoms = 1110 nbur = 1684 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 381 mr = 4212 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2100000 number of dielectric boundary points 3531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2260 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9135 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2722306E-10 1.0341213E-08 midg,1,midg; midg,igrid,midg -1.1170547E-08 1.6543575E-08 1,midg,midg; igrid,midg,midg -2.7480407E-08 3.3054025E-08 gauss-seidel spectral radius is 0.9873924 estimated iterations to convergence 73 setup time was (sec) 0.4000000 now iterating at: 03:45:05 rms-change max change #iterations 0.1502766 19.95975 at 10iterations 1.5089566E-02 2.228287 at 20iterations 1.5027669E-03 0.2033992 at 30iterations 1.6738966E-04 2.1081924E-02 at 40iterations 2.4169638E-05 3.8318634E-03 at 50iterations finished qdiffx linear iterations at : 03:45:08 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.4169638E-05 3.8318634E-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) 3.410000 DelPhi exited at 03:45:09 3.415u 0.176s 0:03.98 89.9% 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 Tue Oct 11 2011 at 03:45:09 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2794 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.922488 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): -10.61200 36.61900 ymin,ymax (A): -26.45600 23.38700 zmin,zma (A): -10.32600 45.22700 x,y,z range (A): 47.23100 49.84300 55.55300 scale (grids/A): 1.922488 object centre (A): 13.00350 -1.534500 17.45050 number of atom coordinates read : 2794 total number of charged atoms : 2641 net assigned charge : 2.162019 assigned positive charge : 423.4436 centred at (gu) : 90.17140 89.67208 95.37808 assigned negative charge : -421.2823 centred at (gu) : 89.46909 89.34878 95.28833 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22617 grid for indexing accessible points = 1.400000 m= 28929 mr = 56942 m= 4354 mr = 21574 m= 229 mr = 2706 m= 3 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 993 time to turn everything in is 0.3900000 number of dielectric boundary points 32689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20789 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) : 0.6408294 object centre at (A) : 13.00350 -1.534500 17.45050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5837971E-02 7.0691956E-03 midg,1,midg; midg,igrid,midg -1.7060105E-02 -5.0281165E-03 1,midg,midg; igrid,midg,midg -1.1583404E-02 5.2871961E-02 gauss-seidel spectral radius is 0.9986723 estimated iterations to convergence 217 setup time was (sec) 0.6100000 now iterating at: 03:45:10 rms-change max change #iterations 4.543188 183.0245 at 10iterations 2.143292 68.97110 at 20iterations 1.017988 33.44743 at 30iterations 0.4843504 15.66513 at 40iterations 0.2294592 6.898041 at 50iterations 0.1089478 3.683678 at 60iterations 5.1692680E-02 1.517319 at 70iterations 2.4521405E-02 0.7669411 at 80iterations 1.1625309E-02 0.3445358 at 90iterations 5.5123325E-03 0.1665764 at 100iterations 2.6100031E-03 7.5656891E-02 at 110iterations 1.2377879E-03 3.6830902E-02 at 120iterations finished qdiffx linear iterations at : 03:45:17 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 1.2377879E-03 3.6830902E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 03:45:17 7.890u 0.200s 0:08.42 96.0% 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 03:45:17 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2794 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.883733 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): -10.61200 36.61900 ymin,ymax (A): -26.45600 23.38700 zmin,zma (A): -10.32600 45.22700 x,y,z range (A): 47.23100 49.84300 55.55300 scale (grids/A): 2.883733 object centre (A): 13.00350 -1.534500 17.45050 number of atom coordinates read : 2794 total number of charged atoms : 2641 net assigned charge : 2.162019 assigned positive charge : 423.4436 centred at (gu) : 90.25689 89.50798 98.06694 assigned negative charge : -421.2823 centred at (gu) : 89.20354 89.02306 97.93258 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 186298 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22617 grid for indexing accessible points = 1.400000 m= 94453 mr = 137947 m= 33124 mr = 77880 m= 7662 mr = 26736 m= 1013 mr = 5687 m= 60 mr = 668 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 3149 time to turn everything in is 1.020000 number of dielectric boundary points 73670 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 21112 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) : 1.922488 object centre at (A) : 13.00350 -1.534500 17.45050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4322560 0.2295625 midg,1,midg; midg,igrid,midg -0.1953985 -0.1398922 1,midg,midg; igrid,midg,midg -5.6784533E-02 0.4809807 gauss-seidel spectral radius is 0.9992664 estimated iterations to convergence 291 setup time was (sec) 1.260000 now iterating at: 03:45:19 rms-change max change #iterations 10.53084 335.7123 at 10iterations 6.143267 170.2239 at 20iterations 3.573622 82.22707 at 30iterations 2.074632 39.83184 at 40iterations 1.200889 23.53353 at 50iterations 0.6963640 14.15091 at 60iterations 0.4018618 7.324512 at 70iterations 0.2325798 4.488605 at 80iterations 0.1345549 2.567540 at 90iterations 7.7611543E-02 1.524303 at 100iterations 4.4743787E-02 0.8788385 at 110iterations 2.5797686E-02 0.4571247 at 120iterations 1.4879514E-02 0.2627630 at 130iterations 8.5969428E-03 0.1533928 at 140iterations 4.9482123E-03 9.2292786E-02 at 150iterations 2.8604206E-03 4.9684495E-02 at 160iterations 1.6458356E-03 2.9634476E-02 at 170iterations 9.5069822E-04 1.7227173E-02 at 180iterations finished qdiffx linear iterations at : 03:45:30 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 9.5069822E-04 1.7227173E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 03:45:31 12.868u 0.205s 0:13.48 96.8% 0+0k 0+0io 0pf+0w