Wed Dec 28 11:02:38 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+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 Wed Dec 28 2011 at 11:02:38 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: 228 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: 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 : 2.000006 assigned positive charge : 290.1940 centred at (gu) : 90.02225 90.02645 90.36575 assigned negative charge : -288.1943 centred at (gu) : 90.03084 90.14335 90.53424 start vw surface at 0.1800000 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 = 0.1300000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3200000 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 0.4600000 number of grid points assigned charge 5787 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4244355E-09 -3.7011654E-09 midg,1,midg; midg,igrid,midg 3.5755208E-09 -2.1095869E-09 1,midg,midg; igrid,midg,midg 9.9321562E-10 5.8257432E-10 gauss-seidel spectral radius is 0.9854054 estimated iterations to convergence 68 setup time was (sec) 0.6000000 now iterating at: 11:02:39 rms-change max change #iterations 9.0972297E-02 20.99611 at 10iterations 7.5856601E-03 1.372256 at 20iterations 6.3128211E-04 0.1215134 at 30iterations 5.1792791E-05 9.9773407E-03 at 40iterations 4.2854331E-06 6.7138672E-04 at 50iterations finished qdiffx linear iterations at : 11:02:42 total time elapsed so far: 3.720000 # loops : 50 mean,max change (kT/e) : 4.2854331E-06 6.7138672E-04 energy calculations done at 3.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.950000 DelPhi exited at 11:02:43 3.951u 0.166s 0:04.78 85.9% 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 Wed Dec 28 2011 at 11:02:43 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: 228 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 : 2.000006 assigned positive charge : 290.1940 centred at (gu) : 90.06680 90.07935 91.09734 assigned negative charge : -288.1943 centred at (gu) : 90.09253 90.42999 91.60294 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 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 7.1373386E-03 -8.4323902E-03 midg,1,midg; midg,igrid,midg 7.9358770E-03 -4.8318473E-03 1,midg,midg; igrid,midg,midg 3.4598049E-02 2.6833618E-02 gauss-seidel spectral radius is 0.9983797 estimated iterations to convergence 197 setup time was (sec) 0.8300000 now iterating at: 11:02:44 rms-change max change #iterations 3.155370 142.4197 at 10iterations 1.380808 62.50098 at 20iterations 0.6043989 23.59776 at 30iterations 0.2629890 10.60365 at 40iterations 0.1153795 4.374680 at 50iterations 5.0380155E-02 1.949972 at 60iterations 2.1899723E-02 0.8399639 at 70iterations 9.6604684E-03 0.3737907 at 80iterations 4.2062239E-03 0.1746140 at 90iterations 1.8439996E-03 6.6114426E-02 at 100iterations 8.0587715E-04 2.9493332E-02 at 110iterations 3.5359256E-04 1.5241623E-02 at 120iterations finished qdiffx linear iterations at : 11:02:52 total time elapsed so far: 8.420000 # loops : 120 mean,max change (kT/e) : 3.5359256E-04 1.5241623E-02 energy calculations done at 8.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.650000 DelPhi exited at 11:02:53 8.651u 0.200s 0:09.24 95.7% 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 11:02:53 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: 228 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 : 2.000006 assigned positive charge : 290.1940 centred at (gu) : 90.10027 90.11908 91.64600 assigned negative charge : -288.1943 centred at (gu) : 90.13885 90.64499 92.40448 start vw surface at 0.1800000 fill in re-entrant regions at 0.4300000 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 = 0.7000000 no. cavity mid-points inaccessible to solvent = 1436 time to turn everything in is 1.210000 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 1.360000 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 6.2381402E-02 -7.7108890E-02 midg,1,midg; midg,igrid,midg 7.2113678E-02 -4.7049887E-02 1,midg,midg; igrid,midg,midg 0.4411005 0.4239580 gauss-seidel spectral radius is 0.9991681 estimated iterations to convergence 274 setup time was (sec) 1.550000 now iterating at: 11:02:54 rms-change max change #iterations 7.685168 249.6785 at 10iterations 4.332995 114.3846 at 20iterations 2.430456 60.17584 at 30iterations 1.358146 30.25914 at 40iterations 0.7565631 17.28146 at 50iterations 0.4213235 9.681480 at 60iterations 0.2342719 5.387794 at 70iterations 0.1303958 3.026597 at 80iterations 7.2379924E-02 1.580168 at 90iterations 4.0176969E-02 0.8964500 at 100iterations 2.2351054E-02 0.5080222 at 110iterations 1.2438259E-02 0.2746840 at 120iterations 6.8916399E-03 0.1490822 at 130iterations 3.8219674E-03 8.1954956E-02 at 140iterations 2.1204546E-03 5.3470612E-02 at 150iterations 1.1782967E-03 2.5829792E-02 at 160iterations 6.5252720E-04 1.5924454E-02 at 170iterations 3.6266923E-04 7.5225830E-03 at 180iterations finished qdiffx linear iterations at : 11:03:06 total time elapsed so far: 13.42000 # loops : 180 mean,max change (kT/e) : 3.6266923E-04 7.5225830E-03 energy calculations done at 13.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.66000 DelPhi exited at 11:03:07 13.659u 0.221s 0:14.64 94.7% 0+0k 0+0io 0pf+0w