Tue Oct 11 00:55:11 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 00:55:11 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 = 2673 !!! WARNING: ASP 298 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6196045 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): 23.09900 79.34000 ymin,ymax (A): 2.013000 59.46900 zmin,zma (A): 27.18700 69.30900 x,y,z range (A): 56.24100 57.45600 42.12200 scale (grids/A): 0.6196045 object centre (A): 51.21950 30.74100 48.24800 number of atom coordinates read : 2673 total number of charged atoms : 2562 net assigned charge : 6.228019 assigned positive charge : 406.7926 centred at (gu) : 90.61463 90.21592 90.14371 assigned negative charge : -400.5653 centred at (gu) : 90.41033 90.38175 90.31709 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6884 nv = 96 ne = 84 npr = 53207 no. pairs analyzed = 53207 no. exposed pairs = 3223 no. arc points = 22674 no. surface atoms = 1080 nbur = 1593 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3934 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.4000000 number of dielectric boundary points 3271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2261 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 8433 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5964090E-08 -7.2947528E-09 midg,1,midg; midg,igrid,midg 1.5241875E-08 -6.8600827E-09 1,midg,midg; igrid,midg,midg -8.0205469E-09 2.1195191E-08 gauss-seidel spectral radius is 0.9865152 estimated iterations to convergence 70 setup time was (sec) 0.6800000 now iterating at: 00:55:12 rms-change max change #iterations 0.1262392 18.95708 at 10iterations 1.2023319E-02 1.808270 at 20iterations 1.6070612E-03 0.3175087 at 30iterations 4.0943339E-04 9.4696045E-02 at 40iterations 1.2373991E-04 2.9911041E-02 at 50iterations finished qdiffx linear iterations at : 00:55:15 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 1.2373991E-04 2.9911041E-02 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 00:55:16 4.099u 0.176s 0:04.85 87.8% 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 00:55:16 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 = 2673 !!! WARNING: ASP 298 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.858814 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): 23.09900 79.34000 ymin,ymax (A): 2.013000 59.46900 zmin,zma (A): 27.18700 69.30900 x,y,z range (A): 56.24100 57.45600 42.12200 scale (grids/A): 1.858814 object centre (A): 51.21950 30.74100 48.24800 number of atom coordinates read : 2673 total number of charged atoms : 2562 net assigned charge : 6.228019 assigned positive charge : 406.7926 centred at (gu) : 91.84379 90.64725 90.43048 assigned negative charge : -400.5653 centred at (gu) : 91.23057 91.14501 90.95096 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 75082 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22674 grid for indexing accessible points = 1.400000 m= 27271 mr = 53137 m= 4122 mr = 20527 m= 193 mr = 2632 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 2551 time to turn everything in is 0.6700000 number of dielectric boundary points 30315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 20087 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) : 0.6196045 object centre at (A) : 51.21950 30.74100 48.24800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9040968E-02 7.5072404E-03 midg,1,midg; midg,igrid,midg 2.6014287E-02 -6.0328551E-02 1,midg,midg; igrid,midg,midg -1.4936733E-02 7.9370283E-02 gauss-seidel spectral radius is 0.9985734 estimated iterations to convergence 210 setup time was (sec) 1.030000 now iterating at: 00:55:17 rms-change max change #iterations 4.116271 182.6359 at 10iterations 1.881278 70.38915 at 20iterations 0.8659725 29.56413 at 30iterations 0.4003879 12.26464 at 40iterations 0.1840167 5.870421 at 50iterations 8.5076682E-02 2.804417 at 60iterations 3.9315347E-02 1.314196 at 70iterations 1.8206205E-02 0.6326828 at 80iterations 8.5507464E-03 0.2680779 at 90iterations 4.0596901E-03 0.1358871 at 100iterations 1.9981705E-03 7.4409485E-02 at 110iterations 1.0392210E-03 4.0210724E-02 at 120iterations finished qdiffx linear iterations at : 00:55:25 total time elapsed so far: 9.110000 # loops : 120 mean,max change (kT/e) : 1.0392210E-03 4.0210724E-02 energy calculations done at 9.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.350000 DelPhi exited at 00:55:26 9.355u 0.218s 0:10.20 93.7% 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 Tue Oct 11 2011 at 00:55:26 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 = 2673 !!! WARNING: ASP 298 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.788220 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): 23.09900 79.34000 ymin,ymax (A): 2.013000 59.46900 zmin,zma (A): 27.18700 69.30900 x,y,z range (A): 56.24100 57.45600 42.12200 scale (grids/A): 2.788220 object centre (A): 51.21950 30.74100 48.24800 number of atom coordinates read : 2673 total number of charged atoms : 2562 net assigned charge : 6.228019 assigned positive charge : 406.7926 centred at (gu) : 92.76544 90.97085 90.64546 assigned negative charge : -400.5653 centred at (gu) : 91.84557 91.71745 91.42638 start vw surface at 0.1900000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 173533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22674 grid for indexing accessible points = 1.400000 m= 89223 mr = 128375 m= 31701 mr = 73847 m= 7443 mr = 25886 m= 919 mr = 5754 m= 30 mr = 587 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 8465 time to turn everything in is 1.720000 number of dielectric boundary points 68400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 20496 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) : 1.858814 object centre at (A) : 51.21950 30.74100 48.24800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2941316 0.1240626 midg,1,midg; midg,igrid,midg 0.3255467 -0.8738219 1,midg,midg; igrid,midg,midg -0.1488202 1.025375 gauss-seidel spectral radius is 0.9992404 estimated iterations to convergence 286 setup time was (sec) 2.080000 now iterating at: 00:55:28 rms-change max change #iterations 9.693604 290.5680 at 10iterations 5.605160 150.0052 at 20iterations 3.220750 69.13753 at 30iterations 1.847040 41.81311 at 40iterations 1.060156 20.07673 at 50iterations 0.6042535 11.14976 at 60iterations 0.3460585 7.025085 at 70iterations 0.1978371 3.888401 at 80iterations 0.1127100 2.155731 at 90iterations 6.4539835E-02 1.226238 at 100iterations 3.6848310E-02 0.7611160 at 110iterations 2.1088401E-02 0.3971043 at 120iterations 1.2072599E-02 0.2346230 at 130iterations 6.9450713E-03 0.1458302 at 140iterations 4.0467000E-03 7.9501867E-02 at 150iterations 2.3937051E-03 5.1860809E-02 at 160iterations 1.4634856E-03 3.7082672E-02 at 170iterations 9.3447103E-04 2.1217346E-02 at 180iterations finished qdiffx linear iterations at : 00:55:41 total time elapsed so far: 14.20000 # loops : 180 mean,max change (kT/e) : 9.3447103E-04 2.1217346E-02 energy calculations done at 14.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.45000 DelPhi exited at 00:55:41 14.451u 0.230s 0:15.02 97.7% 0+0k 0+0io 0pf+0w