Wed Dec 21 14:20:54 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 21 2011 at 14:20:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6567175 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): -5.818000 35.15700 ymin,ymax (A): -3.204000 50.57300 zmin,zma (A): -23.19200 31.01700 x,y,z range (A): 40.97500 53.77700 54.20900 scale (grids/A): 0.6567175 object centre (A): 14.66950 23.68450 3.912500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 287.8261 centred at (gu) : 90.86597 92.25587 89.82096 assigned negative charge : -283.8263 centred at (gu) : 90.94713 92.35339 89.77671 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5932 nv = 96 ne = 84 npr = 39946 no. pairs analyzed = 39946 no. exposed pairs = 2377 no. arc points = 17091 no. surface atoms = 812 nbur = 1150 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 325 mr = 3379 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.1600000 number of dielectric boundary points 2822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1696 ## 169 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6720 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9573771E-09 1.4952461E-08 midg,1,midg; midg,igrid,midg 1.4115578E-08 -5.8084799E-09 1,midg,midg; igrid,midg,midg 1.6990404E-08 -1.4518664E-09 gauss-seidel spectral radius is 0.9879277 estimated iterations to convergence 74 setup time was (sec) 0.3500000 now iterating at: 14:20:55 rms-change max change #iterations 0.1355080 19.45920 at 10iterations 1.4382795E-02 2.103306 at 20iterations 1.4635633E-03 0.2265796 at 30iterations 1.5412457E-04 2.4510384E-02 at 40iterations 1.6590146E-05 2.4929047E-03 at 50iterations finished qdiffx linear iterations at : 14:20:58 total time elapsed so far: 3.800000 # loops : 50 mean,max change (kT/e) : 1.6590146E-05 2.4929047E-03 energy calculations done at 3.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.920000 DelPhi exited at 14:20:59 3.927u 0.221s 0:04.81 86.0% 0+0k 0+0io 6pf+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 21 2011 at 14:20:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.970153 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): -5.818000 35.15700 ymin,ymax (A): -3.204000 50.57300 zmin,zma (A): -23.19200 31.01700 x,y,z range (A): 40.97500 53.77700 54.20900 scale (grids/A): 1.970153 object centre (A): 14.66950 23.68450 3.912500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 287.8261 centred at (gu) : 92.59805 96.76762 89.46297 assigned negative charge : -283.8263 centred at (gu) : 92.84159 97.06040 89.33037 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 62841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17091 grid for indexing accessible points = 1.400000 m= 25188 mr = 43827 m= 4524 mr = 19735 m= 313 mr = 3116 m= 3 mr = 156 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1389 time to turn everything in is 0.4000000 number of dielectric boundary points 26035 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 14496 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) : 0.6567175 object centre at (A) : 14.66950 23.68450 3.912500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4762135E-02 1.5317129E-02 midg,1,midg; midg,igrid,midg 3.9810997E-02 2.2997900E-03 1,midg,midg; igrid,midg,midg 8.1991218E-03 -3.3749004E-03 gauss-seidel spectral radius is 0.9986458 estimated iterations to convergence 215 setup time was (sec) 0.8000000 now iterating at: 14:21:00 rms-change max change #iterations 3.778508 219.4515 at 10iterations 1.777460 66.36261 at 20iterations 0.8353109 30.64995 at 30iterations 0.3910460 14.03281 at 40iterations 0.1845252 6.312298 at 50iterations 8.6447410E-02 3.015339 at 60iterations 4.0445291E-02 1.267395 at 70iterations 1.9044295E-02 0.6687737 at 80iterations 8.9490097E-03 0.3045197 at 90iterations 4.1954326E-03 0.1494446 at 100iterations 1.9697717E-03 7.2639465E-02 at 110iterations 9.2726451E-04 3.5985947E-02 at 120iterations finished qdiffx linear iterations at : 14:21:09 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 9.2726451E-04 3.5985947E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.520000 DelPhi exited at 14:21:09 9.520u 0.502s 0:10.33 96.9% 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 21 2011 at 14:21:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.955229 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): -5.818000 35.15700 ymin,ymax (A): -3.204000 50.57300 zmin,zma (A): -23.19200 31.01700 x,y,z range (A): 40.97500 53.77700 54.20900 scale (grids/A): 2.955229 object centre (A): 14.66950 23.68450 3.912500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 287.8261 centred at (gu) : 93.89693 100.1514 89.19443 assigned negative charge : -283.8263 centred at (gu) : 94.26250 100.5906 88.99557 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 144830 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17091 grid for indexing accessible points = 1.400000 m= 78277 mr = 105270 m= 32087 mr = 65905 m= 8232 mr = 27304 m= 1341 mr = 6601 m= 105 mr = 967 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 4618 time to turn everything in is 1.090000 number of dielectric boundary points 58757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 14639 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) : 1.970153 object centre at (A) : 14.66950 23.68450 3.912500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8854381 5.1811256E-02 midg,1,midg; midg,igrid,midg 0.3485332 -7.0821226E-02 1,midg,midg; igrid,midg,midg 3.9588653E-02 -1.9161217E-02 gauss-seidel spectral radius is 0.9992492 estimated iterations to convergence 288 setup time was (sec) 1.610000 now iterating at: 14:21:11 rms-change max change #iterations 8.821157 412.2948 at 10iterations 5.100661 136.6216 at 20iterations 2.924606 69.88082 at 30iterations 1.681025 35.80026 at 40iterations 0.9669567 19.59560 at 50iterations 0.5520287 11.27293 at 60iterations 0.3161719 6.294454 at 70iterations 0.1808272 3.941972 at 80iterations 0.1034718 2.199806 at 90iterations 5.9200197E-02 1.364039 at 100iterations 3.3742979E-02 0.6494446 at 110iterations 1.9342605E-02 0.3662648 at 120iterations 1.1038614E-02 0.2409363 at 130iterations 6.3048122E-03 0.1202202 at 140iterations 3.5947498E-03 6.9863319E-02 at 150iterations 2.0575777E-03 4.4421226E-02 at 160iterations 1.1763192E-03 2.2590637E-02 at 170iterations 6.7186891E-04 1.2262702E-02 at 180iterations finished qdiffx linear iterations at : 14:21:26 total time elapsed so far: 15.46000 # loops : 180 mean,max change (kT/e) : 6.7186891E-04 1.2262702E-02 energy calculations done at 15.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.59000 DelPhi exited at 14:21:30 15.587u 0.673s 0:21.46 75.7% 0+0k 0+0io 0pf+0w