Mon Oct 10 19:32:12 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 19:32:12 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 = 2856 !!! WARNING: TYR 271 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5620106 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): 1.906000 56.99900 ymin,ymax (A): -14.31500 34.70200 zmin,zma (A): 29.04300 92.38700 x,y,z range (A): 55.09300 49.01700 63.34400 scale (grids/A): 0.5620106 object centre (A): 29.45250 10.19350 60.71500 number of atom coordinates read : 2856 total number of charged atoms : 2717 net assigned charge : 9.228023 assigned positive charge : 424.0453 centred at (gu) : 88.47575 88.56729 91.11128 assigned negative charge : -414.8185 centred at (gu) : 88.57529 88.57129 91.23665 start vw surface at 0.2200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 5710 nv = 96 ne = 84 npr = 57812 no. pairs analyzed = 57812 no. exposed pairs = 3985 no. arc points = 27612 no. surface atoms = 1328 nbur = 1528 mkacc time = 0.1200000 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 = 1.540000 m= 263 mr = 2643 m= 3 mr = 10 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 0.3800000 number of dielectric boundary points 3323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2765 ## 297 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7450 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8500961E-09 -4.8476340E-10 midg,1,midg; midg,igrid,midg 1.5339645E-09 7.2226614E-10 1,midg,midg; igrid,midg,midg 3.0848033E-09 -2.9317479E-11 gauss-seidel spectral radius is 0.9836614 estimated iterations to convergence 64 setup time was (sec) 0.5800000 now iterating at: 19:32:13 rms-change max change #iterations 7.9767890E-02 12.75927 at 10iterations 5.9461566E-03 1.037121 at 20iterations 7.0908386E-04 0.1539383 at 30iterations 1.8213592E-04 4.8437119E-02 at 40iterations 5.6797537E-05 1.5499115E-02 at 50iterations finished qdiffx linear iterations at : 19:32:16 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 5.6797537E-05 1.5499115E-02 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 19:32:16 3.232u 0.169s 0:03.87 87.5% 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 Mon Oct 10 2011 at 19:32:16 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 = 2856 !!! WARNING: TYR 271 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.686032 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): 1.906000 56.99900 ymin,ymax (A): -14.31500 34.70200 zmin,zma (A): 29.04300 92.38700 x,y,z range (A): 55.09300 49.01700 63.34400 scale (grids/A): 1.686032 object centre (A): 29.45250 10.19350 60.71500 number of atom coordinates read : 2856 total number of charged atoms : 2717 net assigned charge : 9.228023 assigned positive charge : 424.0453 centred at (gu) : 85.42646 85.70080 93.33318 assigned negative charge : -414.8185 centred at (gu) : 85.72541 85.71360 93.70977 start vw surface at 0.2700000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 62052 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27612 grid for indexing accessible points = 1.400000 m= 18687 mr = 39287 m= 2310 mr = 12108 m= 107 mr = 1080 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 30668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 249 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 20988 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) : 0.5620106 object centre at (A) : 29.45250 10.19350 60.71500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4421055E-02 -2.7518038E-02 midg,1,midg; midg,igrid,midg 1.2558904E-02 5.8703097E-03 1,midg,midg; igrid,midg,midg 1.8810965E-02 1.4873873E-02 gauss-seidel spectral radius is 0.9982854 estimated iterations to convergence 192 setup time was (sec) 0.8400000 now iterating at: 19:32:17 rms-change max change #iterations 3.404624 199.6219 at 10iterations 1.437873 60.68982 at 20iterations 0.6147187 24.00520 at 30iterations 0.2625162 9.833803 at 40iterations 0.1115446 3.925554 at 50iterations 4.7601201E-02 1.661667 at 60iterations 2.0338843E-02 0.8561077 at 70iterations 8.7810336E-03 0.3221378 at 80iterations 3.8031847E-03 0.1513214 at 90iterations 1.7026172E-03 7.2055817E-02 at 100iterations 7.9621485E-04 3.2417297E-02 at 110iterations 4.0954788E-04 1.9275665E-02 at 120iterations finished qdiffx linear iterations at : 19:32:24 total time elapsed so far: 7.120000 # loops : 120 mean,max change (kT/e) : 4.0954788E-04 1.9275665E-02 energy calculations done at 7.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 19:32:24 7.294u 0.202s 0:07.81 95.9% 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 Mon Oct 10 2011 at 19:32:24 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 = 2856 !!! WARNING: TYR 271 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.529048 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): 1.906000 56.99900 ymin,ymax (A): -14.31500 34.70200 zmin,zma (A): 29.04300 92.38700 x,y,z range (A): 55.09300 49.01700 63.34400 scale (grids/A): 2.529048 object centre (A): 29.45250 10.19350 60.71500 number of atom coordinates read : 2856 total number of charged atoms : 2717 net assigned charge : 9.228023 assigned positive charge : 424.0453 centred at (gu) : 83.13968 83.55097 94.99963 assigned negative charge : -414.8185 centred at (gu) : 83.58805 83.57039 95.56444 start vw surface at 0.1500000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 144116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27612 grid for indexing accessible points = 1.400000 m= 63023 mr = 97180 m= 19377 mr = 47540 m= 3516 mr = 14052 m= 303 mr = 2226 m= 7 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 69199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 21723 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) : 1.686032 object centre at (A) : 29.45250 10.19350 60.71500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4284849 -0.6317350 midg,1,midg; midg,igrid,midg 0.1960162 8.1549980E-02 1,midg,midg; igrid,midg,midg 0.2028230 0.3212109 gauss-seidel spectral radius is 0.9991637 estimated iterations to convergence 273 setup time was (sec) 1.420000 now iterating at: 19:32:26 rms-change max change #iterations 8.711485 336.7202 at 10iterations 4.940079 109.5064 at 20iterations 2.783305 67.53901 at 30iterations 1.566314 36.15370 at 40iterations 0.8758892 20.13936 at 50iterations 0.4910045 10.43339 at 60iterations 0.2735610 5.780570 at 70iterations 0.1522545 3.198409 at 80iterations 8.4754787E-02 2.010139 at 90iterations 4.7196392E-02 1.045158 at 100iterations 2.6307570E-02 0.5583496 at 110iterations 1.4622576E-02 0.3167419 at 120iterations 8.1774779E-03 0.1705914 at 130iterations 4.6049859E-03 0.1005993 at 140iterations 2.6203098E-03 5.9747696E-02 at 150iterations 1.5196137E-03 3.5480499E-02 at 160iterations 9.1745559E-04 2.4137497E-02 at 170iterations 5.8414624E-04 1.6267776E-02 at 180iterations finished qdiffx linear iterations at : 19:32:37 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 5.8414624E-04 1.6267776E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.14000 DelPhi exited at 19:32:39 13.141u 0.185s 0:14.59 91.2% 0+0k 0+0io 0pf+0w