Tue Oct 11 04:47:41 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 04:47:41 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2234 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: 0.6355100 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): 0.4910001 56.50900 ymin,ymax (A): -19.52300 23.19500 zmin,zma (A): -30.52600 19.43000 x,y,z range (A): 56.01800 42.71800 49.95600 scale (grids/A): 0.6355100 object centre (A): 28.50000 1.836000 -5.547999 number of atom coordinates read : 2234 total number of charged atoms : 2098 net assigned charge : 4.500010 assigned positive charge : 330.6146 centred at (gu) : 90.84900 90.67728 89.94939 assigned negative charge : -326.1148 centred at (gu) : 90.98522 90.87462 89.90946 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6093 nv = 96 ne = 84 npr = 44672 no. pairs analyzed = 44672 no. exposed pairs = 2859 no. arc points = 20688 no. surface atoms = 964 nbur = 1270 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 311 mr = 3194 m= 5 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.2600000 number of dielectric boundary points 3181 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2000 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7249 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5765452E-09 9.3602939E-09 midg,1,midg; midg,igrid,midg 1.9645668E-08 -1.3331875E-08 1,midg,midg; igrid,midg,midg 1.4698095E-08 -7.2438073E-09 gauss-seidel spectral radius is 0.9871440 estimated iterations to convergence 72 setup time was (sec) 0.4900000 now iterating at: 04:47:42 rms-change max change #iterations 0.1288549 22.21495 at 10iterations 1.2621620E-02 1.837345 at 20iterations 1.2107706E-03 0.1975327 at 30iterations 1.1806699E-04 1.9192696E-02 at 40iterations 1.1462324E-05 1.6174316E-03 at 50iterations finished qdiffx linear iterations at : 04:47:44 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.1462324E-05 1.6174316E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 04:47:45 3.308u 0.231s 0:03.93 89.8% 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 04:47:45 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2234 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: 1.906530 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): 0.4910001 56.50900 ymin,ymax (A): -19.52300 23.19500 zmin,zma (A): -30.52600 19.43000 x,y,z range (A): 56.01800 42.71800 49.95600 scale (grids/A): 1.906530 object centre (A): 28.50000 1.836000 -5.547999 number of atom coordinates read : 2234 total number of charged atoms : 2098 net assigned charge : 4.500010 assigned positive charge : 330.6146 centred at (gu) : 92.54668 92.03146 89.84791 assigned negative charge : -326.1148 centred at (gu) : 92.95554 92.62386 89.72829 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 65361 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20688 grid for indexing accessible points = 1.400000 m= 22600 mr = 44160 m= 3424 mr = 16185 m= 209 mr = 2070 m= 4 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1661 time to turn everything in is 0.4800000 number of dielectric boundary points 29119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 95 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 16494 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) : 0.6355100 object centre at (A) : 28.50000 1.836000 -5.547999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1197452E-02 1.0798778E-02 midg,1,midg; midg,igrid,midg 2.1261359E-02 -9.2064049E-03 1,midg,midg; igrid,midg,midg 5.9170902E-02 2.4497311E-03 gauss-seidel spectral radius is 0.9986042 estimated iterations to convergence 212 setup time was (sec) 0.7800000 now iterating at: 04:47:46 rms-change max change #iterations 3.862155 169.5061 at 10iterations 1.789770 68.22189 at 20iterations 0.8313233 33.15158 at 30iterations 0.3841842 13.45233 at 40iterations 0.1784071 6.219863 at 50iterations 8.2425781E-02 2.798899 at 60iterations 3.8405679E-02 1.417328 at 70iterations 1.7747847E-02 0.6678162 at 80iterations 8.2458165E-03 0.2733555 at 90iterations 3.8408919E-03 0.1436214 at 100iterations 1.7803864E-03 6.1666489E-02 at 110iterations 8.2876044E-04 2.6767731E-02 at 120iterations finished qdiffx linear iterations at : 04:47:52 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 8.2876044E-04 2.6767731E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 04:47:53 7.593u 0.243s 0:08.65 90.5% 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 04:47:54 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2234 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.859795 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): 0.4910001 56.50900 ymin,ymax (A): -19.52300 23.19500 zmin,zma (A): -30.52600 19.43000 x,y,z range (A): 56.01800 42.71800 49.95600 scale (grids/A): 2.859795 object centre (A): 28.50000 1.836000 -5.547999 number of atom coordinates read : 2234 total number of charged atoms : 2098 net assigned charge : 4.500010 assigned positive charge : 330.6146 centred at (gu) : 93.81978 93.04707 89.77180 assigned negative charge : -326.1148 centred at (gu) : 94.43332 93.93586 89.59243 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 151053 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20688 grid for indexing accessible points = 1.400000 m= 73911 mr = 107178 m= 25694 mr = 59510 m= 6110 mr = 20137 m= 834 mr = 4455 m= 36 mr = 536 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 5886 time to turn everything in is 1.180000 number of dielectric boundary points 65811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 16780 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) : 1.906530 object centre at (A) : 28.50000 1.836000 -5.547999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1456269 0.1233524 midg,1,midg; midg,igrid,midg 0.2153720 -5.7884097E-02 1,midg,midg; igrid,midg,midg 0.8883646 -0.2463298 gauss-seidel spectral radius is 0.9992509 estimated iterations to convergence 288 setup time was (sec) 1.480000 now iterating at: 04:47:55 rms-change max change #iterations 9.164535 640.5148 at 10iterations 5.345492 123.3006 at 20iterations 3.098561 76.86767 at 30iterations 1.789404 38.31522 at 40iterations 1.031055 21.54025 at 50iterations 0.5925806 12.48637 at 60iterations 0.3402543 6.893786 at 70iterations 0.1951942 3.906395 at 80iterations 0.1119679 2.178415 at 90iterations 6.4071670E-02 1.399378 at 100iterations 3.6736138E-02 0.7770004 at 110iterations 2.1011665E-02 0.4244728 at 120iterations 1.2064801E-02 0.2238865 at 130iterations 6.8952832E-03 0.1376343 at 140iterations 3.9387415E-03 7.8090668E-02 at 150iterations 2.2596265E-03 4.7174454E-02 at 160iterations 1.2901375E-03 2.3243677E-02 at 170iterations 7.3766167E-04 1.3875484E-02 at 180iterations finished qdiffx linear iterations at : 04:48:06 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 7.3766167E-04 1.3875484E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 04:48:07 12.363u 0.283s 0:13.06 96.7% 0+0k 0+0io 0pf+0w