Mon Oct 10 17:04:17 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 Mon Oct 10 2011 at 17:04:17 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2572 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: 0.6134652 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): 9.707000 60.87700 ymin,ymax (A): 8.746000 57.35400 zmin,zma (A): 9.040000 67.07100 x,y,z range (A): 51.17000 48.60800 58.03100 scale (grids/A): 0.6134652 object centre (A): 35.29200 33.05000 38.05550 number of atom coordinates read : 2572 total number of charged atoms : 2406 net assigned charge : 4.500022 assigned positive charge : 375.7360 centred at (gu) : 90.64905 89.36974 89.22633 assigned negative charge : -371.2365 centred at (gu) : 90.55841 89.40289 89.35062 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6717 nv = 96 ne = 84 npr = 51115 no. pairs analyzed = 51115 no. exposed pairs = 3448 no. arc points = 24729 no. surface atoms = 1165 nbur = 1407 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3570 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2361 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7976 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1048509E-08 -3.1280576E-09 midg,1,midg; midg,igrid,midg 5.2767644E-09 9.8633313E-10 1,midg,midg; igrid,midg,midg -1.6585896E-09 8.7460563E-09 gauss-seidel spectral radius is 0.9862500 estimated iterations to convergence 70 setup time was (sec) 0.4100000 now iterating at: 17:04:17 rms-change max change #iterations 0.1191970 17.23239 at 10iterations 1.0438894E-02 1.484749 at 20iterations 9.6778735E-04 0.1890429 at 30iterations 8.7821310E-05 1.3282776E-02 at 40iterations 9.3724511E-06 1.4839172E-03 at 50iterations finished qdiffx linear iterations at : 17:04:20 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 9.3724511E-06 1.4839172E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 17:04:22 3.446u 0.183s 0:05.04 71.8% 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 Mon Oct 10 2011 at 17:04:22 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2572 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: 1.840396 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): 9.707000 60.87700 ymin,ymax (A): 8.746000 57.35400 zmin,zma (A): 9.040000 67.07100 x,y,z range (A): 51.17000 48.60800 58.03100 scale (grids/A): 1.840396 object centre (A): 35.29200 33.05000 38.05550 number of atom coordinates read : 2572 total number of charged atoms : 2406 net assigned charge : 4.500022 assigned positive charge : 375.7360 centred at (gu) : 91.94672 88.10870 87.67835 assigned negative charge : -371.2365 centred at (gu) : 91.67500 88.20843 88.05148 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72733 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24729 grid for indexing accessible points = 1.400000 m= 25404 mr = 49299 m= 3742 mr = 18265 m= 171 mr = 2189 m= 5 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 32257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18872 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) : 0.6134652 object centre at (A) : 35.29200 33.05000 38.05550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0819984E-02 -2.1267027E-02 midg,1,midg; midg,igrid,midg 1.6784253E-02 1.4418347E-02 1,midg,midg; igrid,midg,midg -8.4360586E-03 8.7538566E-03 gauss-seidel spectral radius is 0.9985495 estimated iterations to convergence 208 setup time was (sec) 0.5800000 now iterating at: 17:04:23 rms-change max change #iterations 3.902853 150.8221 at 10iterations 1.781334 59.37946 at 20iterations 0.8155866 28.17198 at 30iterations 0.3726403 12.72366 at 40iterations 0.1698519 6.392284 at 50iterations 7.7683821E-02 2.714264 at 60iterations 3.5657067E-02 1.184042 at 70iterations 1.6310973E-02 0.5594587 at 80iterations 7.4493806E-03 0.2453671 at 90iterations 3.4028334E-03 0.1050830 at 100iterations 1.5628363E-03 5.5136681E-02 at 110iterations 7.1269000E-04 2.2398949E-02 at 120iterations finished qdiffx linear iterations at : 17:04:30 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 7.1269000E-04 2.2398949E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 17:04:31 7.917u 0.217s 0:08.79 92.3% 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 Mon Oct 10 2011 at 17:04:31 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2572 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: 2.760594 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): 9.707000 60.87700 ymin,ymax (A): 8.746000 57.35400 zmin,zma (A): 9.040000 67.07100 x,y,z range (A): 51.17000 48.60800 58.03100 scale (grids/A): 2.760594 object centre (A): 35.29200 33.05000 38.05550 number of atom coordinates read : 2572 total number of charged atoms : 2406 net assigned charge : 4.500022 assigned positive charge : 375.7360 centred at (gu) : 92.91992 87.16290 86.51736 assigned negative charge : -371.2365 centred at (gu) : 92.51244 87.31255 87.07721 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 168282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24729 grid for indexing accessible points = 1.400000 m= 83055 mr = 119941 m= 29112 mr = 66977 m= 6426 mr = 22897 m= 713 mr = 4644 m= 45 mr = 410 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9000000 number of dielectric boundary points 72747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 19247 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) : 1.840396 object centre at (A) : 35.29200 33.05000 38.05550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6683559 -0.2146364 midg,1,midg; midg,igrid,midg 0.1258754 0.1410847 1,midg,midg; igrid,midg,midg -0.1245764 9.7291045E-02 gauss-seidel spectral radius is 0.9992424 estimated iterations to convergence 287 setup time was (sec) 1.140000 now iterating at: 17:04:32 rms-change max change #iterations 9.246269 273.2006 at 10iterations 5.378208 123.2228 at 20iterations 3.089392 71.57273 at 30iterations 1.777673 40.48063 at 40iterations 1.020418 19.24748 at 50iterations 0.5829258 12.14029 at 60iterations 0.3333642 6.693640 at 70iterations 0.1906110 3.750099 at 80iterations 0.1088098 2.194289 at 90iterations 6.2016755E-02 1.182434 at 100iterations 3.5387475E-02 0.6124268 at 110iterations 2.0225110E-02 0.3914871 at 120iterations 1.1535120E-02 0.2149658 at 130iterations 6.5809954E-03 0.1338172 at 140iterations 3.7485820E-03 7.1346283E-02 at 150iterations 2.1405246E-03 3.9594412E-02 at 160iterations 1.2215107E-03 2.3292542E-02 at 170iterations 6.9592323E-04 1.3672829E-02 at 180iterations finished qdiffx linear iterations at : 17:04:43 total time elapsed so far: 12.31000 # loops : 180 mean,max change (kT/e) : 6.9592323E-04 1.3672829E-02 energy calculations done at 12.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.44000 DelPhi exited at 17:04:44 12.441u 0.199s 0:13.27 95.1% 0+0k 0+0io 0pf+0w