Tue Oct 11 03:24:09 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 Tue Oct 11 2011 at 03:24:09 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3067 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5664010 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): -12.69200 38.83300 ymin,ymax (A): -1.756000 51.43300 zmin,zma (A): -17.24100 45.61200 x,y,z range (A): 51.52500 53.18900 62.85300 scale (grids/A): 0.5664010 object centre (A): 13.07050 24.83850 14.18550 number of atom coordinates read : 3067 total number of charged atoms : 2926 net assigned charge : 3.500026 assigned positive charge : 456.0789 centred at (gu) : 89.50887 90.28815 91.15129 assigned negative charge : -452.5802 centred at (gu) : 89.49488 90.33994 91.13552 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6529 nv = 96 ne = 84 npr = 60306 no. pairs analyzed = 60306 no. exposed pairs = 4439 no. arc points = 31477 no. surface atoms = 1464 nbur = 1603 mkacc time = 0.1300000 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 = 1.512000 m= 305 mr = 3023 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3071 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8327 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9275856E-10 9.1116320E-10 midg,1,midg; midg,igrid,midg 1.1178501E-09 -2.8501296E-10 1,midg,midg; igrid,midg,midg 3.0527453E-10 5.9560651E-10 gauss-seidel spectral radius is 0.9839377 estimated iterations to convergence 65 setup time was (sec) 0.5500000 now iterating at: 03:24:10 rms-change max change #iterations 8.8221014E-02 14.01218 at 10iterations 6.8311584E-03 1.013756 at 20iterations 7.4375840E-04 0.1305256 at 30iterations 1.5881509E-04 2.8470993E-02 at 40iterations 4.2888667E-05 8.0242157E-03 at 50iterations finished qdiffx linear iterations at : 03:24:12 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 4.2888667E-05 8.0242157E-03 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 03:24:13 3.183u 0.155s 0:03.70 90.0% 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 03:24:13 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3067 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.699203 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): -12.69200 38.83300 ymin,ymax (A): -1.756000 51.43300 zmin,zma (A): -17.24100 45.61200 x,y,z range (A): 51.52500 53.18900 62.85300 scale (grids/A): 1.699203 object centre (A): 13.07050 24.83850 14.18550 number of atom coordinates read : 3067 total number of charged atoms : 2926 net assigned charge : 3.500026 assigned positive charge : 456.0789 centred at (gu) : 88.52539 90.86338 93.45312 assigned negative charge : -452.5802 centred at (gu) : 88.48424 91.01930 93.40617 start vw surface at 0.2300000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 71012 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31477 grid for indexing accessible points = 1.400000 m= 22264 mr = 45128 m= 2686 mr = 14501 m= 106 mr = 1329 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 35099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 272 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 22584 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) : 0.5664010 object centre at (A) : 13.07050 24.83850 14.18550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1488211E-04 1.0084116E-02 midg,1,midg; midg,igrid,midg 8.2808100E-03 -7.3063727E-03 1,midg,midg; igrid,midg,midg 5.8186445E-03 1.7761696E-02 gauss-seidel spectral radius is 0.9983648 estimated iterations to convergence 196 setup time was (sec) 0.8800000 now iterating at: 03:24:14 rms-change max change #iterations 3.688964 145.1820 at 10iterations 1.592722 58.30710 at 20iterations 0.6919572 26.66463 at 30iterations 0.2997241 11.74917 at 40iterations 0.1308149 4.461428 at 50iterations 5.6873597E-02 2.134007 at 60iterations 2.4820486E-02 1.093037 at 70iterations 1.0837538E-02 0.4162264 at 80iterations 4.7629736E-03 0.1667328 at 90iterations 2.1073001E-03 7.5851440E-02 at 100iterations 9.4232184E-04 3.3349991E-02 at 110iterations 4.3686069E-04 1.5710831E-02 at 120iterations finished qdiffx linear iterations at : 03:24:20 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 4.3686069E-04 1.5710831E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 03:24:21 7.505u 0.191s 0:08.13 94.5% 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 03:24:21 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3067 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.548805 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): -12.69200 38.83300 ymin,ymax (A): -1.756000 51.43300 zmin,zma (A): -17.24100 45.61200 x,y,z range (A): 51.52500 53.18900 62.85300 scale (grids/A): 2.548805 object centre (A): 13.07050 24.83850 14.18550 number of atom coordinates read : 3067 total number of charged atoms : 2926 net assigned charge : 3.500026 assigned positive charge : 456.0789 centred at (gu) : 87.78802 91.29481 95.17955 assigned negative charge : -452.5802 centred at (gu) : 87.72637 91.52882 95.10925 start vw surface at 0.2100000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 164511 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31477 grid for indexing accessible points = 1.400000 m= 74712 mr = 111394 m= 23408 mr = 56777 m= 4384 mr = 17023 m= 395 mr = 2773 m= 7 mr = 188 m= 0 mr = 0 time to grow re-entrant surface = 0.6800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 79262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 23391 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) : 1.699203 object centre at (A) : 13.07050 24.83850 14.18550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5615720E-02 3.4531545E-02 midg,1,midg; midg,igrid,midg 0.1009790 -0.1623451 1,midg,midg; igrid,midg,midg 0.1132203 0.3607590 gauss-seidel spectral radius is 0.9992075 estimated iterations to convergence 280 setup time was (sec) 1.530000 now iterating at: 03:24:22 rms-change max change #iterations 9.436978 280.5599 at 10iterations 5.497707 143.9251 at 20iterations 3.167669 77.50538 at 30iterations 1.819975 43.31795 at 40iterations 1.040360 23.27253 at 50iterations 0.5930176 12.52656 at 60iterations 0.3365598 8.560390 at 70iterations 0.1905916 3.748855 at 80iterations 0.1082965 2.258842 at 90iterations 6.1181407E-02 1.241558 at 100iterations 3.4548096E-02 0.7335892 at 110iterations 1.9582616E-02 0.3994608 at 120iterations 1.1082312E-02 0.2257805 at 130iterations 6.2914100E-03 0.1295156 at 140iterations 3.5790179E-03 7.8804016E-02 at 150iterations 2.0506633E-03 4.2947769E-02 at 160iterations 1.1969226E-03 2.4534225E-02 at 170iterations 7.0986233E-04 1.5199661E-02 at 180iterations finished qdiffx linear iterations at : 03:24:32 total time elapsed so far: 11.26000 # loops : 180 mean,max change (kT/e) : 7.0986233E-04 1.5199661E-02 energy calculations done at 11.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.43000 DelPhi exited at 03:24:33 11.436u 0.204s 0:12.01 96.8% 0+0k 0+0io 0pf+0w