Wed Dec 28 11:03:07 PST 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 Wed Dec 28 2011 at 11:03:08 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1969 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: 0.5965547 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): -24.85400 34.82200 ymin,ymax (A): -18.34300 20.48000 zmin,zma (A): -4.156000 39.09500 x,y,z range (A): 59.67600 38.82300 43.25100 scale (grids/A): 0.5965547 object centre (A): 4.984001 1.068500 17.46950 number of atom coordinates read : 1969 total number of charged atoms : 1837 net assigned charge : 2.000008 assigned positive charge : 292.9940 centred at (gu) : 90.02095 90.01208 90.34118 assigned negative charge : -290.9943 centred at (gu) : 90.03632 90.12058 90.50217 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 4712 nv = 96 ne = 84 npr = 40215 no. pairs analyzed = 40215 no. exposed pairs = 2535 no. arc points = 17313 no. surface atoms = 859 nbur = 1110 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 238 mr = 2549 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3300000 number of dielectric boundary points 2383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1739 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 5787 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3194723E-09 -3.5195140E-09 midg,1,midg; midg,igrid,midg 3.4115859E-09 -1.9209014E-09 1,midg,midg; igrid,midg,midg 1.1583784E-09 4.0965137E-10 gauss-seidel spectral radius is 0.9854054 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 11:03:08 rms-change max change #iterations 9.3146957E-02 20.55102 at 10iterations 7.8123864E-03 1.444885 at 20iterations 6.4804201E-04 0.1136951 at 30iterations 5.3006919E-05 9.1896057E-03 at 40iterations 4.4295698E-06 7.3242188E-04 at 50iterations finished qdiffx linear iterations at : 11:03:11 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 4.4295698E-06 7.3242188E-04 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 11:03:12 3.997u 0.156s 0:04.51 91.7% 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 Wed Dec 28 2011 at 11:03:12 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1969 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.789664 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): -24.85400 34.82200 ymin,ymax (A): -18.34300 20.48000 zmin,zma (A): -4.156000 39.09500 x,y,z range (A): 59.67600 38.82300 43.25100 scale (grids/A): 1.789664 object centre (A): 4.984001 1.068500 17.46950 number of atom coordinates read : 1969 total number of charged atoms : 1837 net assigned charge : 2.000008 assigned positive charge : 292.9940 centred at (gu) : 90.06291 90.03620 91.02361 assigned negative charge : -290.9943 centred at (gu) : 90.10901 90.36172 91.50671 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 50974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17313 grid for indexing accessible points = 1.400000 m= 17621 mr = 34663 m= 2229 mr = 13002 m= 103 mr = 1318 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 404 time to turn everything in is 0.5000000 number of dielectric boundary points 21911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 151 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 14372 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) : 0.5965547 object centre at (A) : 4.984001 1.068500 17.46950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6519636E-03 -7.9495134E-03 midg,1,midg; midg,igrid,midg 7.6084654E-03 -4.3688747E-03 1,midg,midg; igrid,midg,midg 3.4953654E-02 2.6657958E-02 gauss-seidel spectral radius is 0.9983797 estimated iterations to convergence 197 setup time was (sec) 0.8400000 now iterating at: 11:03:13 rms-change max change #iterations 3.202088 142.4197 at 10iterations 1.401074 62.50690 at 20iterations 0.6136565 24.41451 at 30iterations 0.2668665 10.64669 at 40iterations 0.1171004 4.350468 at 50iterations 5.1149122E-02 2.005800 at 60iterations 2.2221047E-02 0.8174314 at 70iterations 9.8013692E-03 0.3846283 at 80iterations 4.2690686E-03 0.1751442 at 90iterations 1.8709084E-03 6.6512108E-02 at 100iterations 8.1772800E-04 2.9798508E-02 at 110iterations 3.5868600E-04 1.4661789E-02 at 120iterations finished qdiffx linear iterations at : 11:03:21 total time elapsed so far: 8.560000 # loops : 120 mean,max change (kT/e) : 3.5868600E-04 1.4661789E-02 energy calculations done at 8.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.820000 DelPhi exited at 11:03:22 8.825u 0.201s 0:09.67 93.2% 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 Wed Dec 28 2011 at 11:03:22 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1969 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.684496 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): -24.85400 34.82200 ymin,ymax (A): -18.34300 20.48000 zmin,zma (A): -4.156000 39.09500 x,y,z range (A): 59.67600 38.82300 43.25100 scale (grids/A): 2.684496 object centre (A): 4.984001 1.068500 17.46950 number of atom coordinates read : 1969 total number of charged atoms : 1837 net assigned charge : 2.000008 assigned positive charge : 292.9940 centred at (gu) : 90.09445 90.05437 91.53541 assigned negative charge : -290.9943 centred at (gu) : 90.16356 90.54260 92.26013 start vw surface at 0.1800000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 117802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17313 grid for indexing accessible points = 1.400000 m= 58185 mr = 84134 m= 19727 mr = 47379 m= 3761 mr = 15956 m= 416 mr = 2713 m= 13 mr = 284 m= 0 mr = 4 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 1436 time to turn everything in is 1.190000 number of dielectric boundary points 49434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 14694 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) : 1.789664 object centre at (A) : 4.984001 1.068500 17.46950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7149045E-02 -7.0677511E-02 midg,1,midg; midg,igrid,midg 6.8255186E-02 -4.1646581E-02 1,midg,midg; igrid,midg,midg 0.4452989 0.4223136 gauss-seidel spectral radius is 0.9991681 estimated iterations to convergence 274 setup time was (sec) 1.580000 now iterating at: 11:03:24 rms-change max change #iterations 7.778066 249.6861 at 10iterations 4.385549 114.3819 at 20iterations 2.458578 60.16251 at 30iterations 1.373516 30.95835 at 40iterations 0.7650732 17.73614 at 50iterations 0.4260494 9.894464 at 60iterations 0.2369772 5.397620 at 70iterations 0.1318258 3.089625 at 80iterations 7.3162250E-02 1.609880 at 90iterations 4.0608931E-02 0.9159756 at 100iterations 2.2590397E-02 0.5099468 at 110iterations 1.2572271E-02 0.2789884 at 120iterations 6.9660186E-03 0.1550293 at 130iterations 3.8629666E-03 8.3679199E-02 at 140iterations 2.1428207E-03 5.2106857E-02 at 150iterations 1.1903829E-03 2.6151180E-02 at 160iterations 6.5946078E-04 1.6379833E-02 at 170iterations 3.6652942E-04 7.6637268E-03 at 180iterations finished qdiffx linear iterations at : 11:03:37 total time elapsed so far: 14.92000 # loops : 180 mean,max change (kT/e) : 3.6652942E-04 7.6637268E-03 energy calculations done at 14.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.17000 DelPhi exited at 11:03:38 15.167u 0.242s 0:15.78 97.5% 0+0k 0+0io 0pf+0w