Sat Oct 8 16:27:30 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 Sat Oct 8 2011 at 16:27:30 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 = 2270 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: 0.6667041 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): -2.119000 47.63600 ymin,ymax (A): -17.75300 28.83400 zmin,zma (A): -18.13700 35.26000 x,y,z range (A): 49.75500 46.58700 53.39700 scale (grids/A): 0.6667041 object centre (A): 22.75850 5.540500 8.561502 number of atom coordinates read : 2270 total number of charged atoms : 2186 net assigned charge : 3.000000 assigned positive charge : 334.3273 centred at (gu) : 89.89934 89.27776 90.08609 assigned negative charge : -331.3279 centred at (gu) : 89.95457 89.41602 90.15990 start vw surface at 0.1100000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6697 nv = 96 ne = 84 npr = 46663 no. pairs analyzed = 46663 no. exposed pairs = 2831 no. arc points = 19272 no. surface atoms = 970 nbur = 1300 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 432 mr = 3746 m= 3 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3310 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1782 ## 121 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7982 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3186564E-08 -6.0858012E-09 midg,1,midg; midg,igrid,midg 4.2103810E-08 -1.6401316E-08 1,midg,midg; igrid,midg,midg 2.0344913E-08 -2.1368414E-09 gauss-seidel spectral radius is 0.9883068 estimated iterations to convergence 75 setup time was (sec) 0.6200000 now iterating at: 16:27:31 rms-change max change #iterations 0.1595638 25.32333 at 10iterations 1.7638290E-02 2.564137 at 20iterations 1.9828966E-03 0.3105392 at 30iterations 2.7665994E-04 4.0897369E-02 at 40iterations 5.7090521E-05 8.6851120E-03 at 50iterations finished qdiffx linear iterations at : 16:27:36 total time elapsed so far: 5.100000 # loops : 50 mean,max change (kT/e) : 5.7090521E-05 8.6851120E-03 energy calculations done at 5.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.260000 DelPhi exited at 16:27:36 5.269u 0.458s 0:06.04 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 Sat Oct 8 2011 at 16:27:36 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 = 2270 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: 2.000112 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): -2.119000 47.63600 ymin,ymax (A): -17.75300 28.83400 zmin,zma (A): -18.13700 35.26000 x,y,z range (A): 49.75500 46.58700 53.39700 scale (grids/A): 2.000112 object centre (A): 22.75850 5.540500 8.561502 number of atom coordinates read : 2270 total number of charged atoms : 2186 net assigned charge : 3.000000 assigned positive charge : 334.3273 centred at (gu) : 89.69781 87.83263 90.25815 assigned negative charge : -331.3279 centred at (gu) : 89.86356 88.24790 90.47974 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71569 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19272 grid for indexing accessible points = 1.400000 m= 27196 mr = 49828 m= 5369 mr = 20329 m= 387 mr = 3697 m= 10 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 390 time to turn everything in is 0.6300000 number of dielectric boundary points 30514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 17276 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) : 0.6667041 object centre at (A) : 22.75850 5.540500 8.561502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9551979E-02 -8.4620612E-03 midg,1,midg; midg,igrid,midg 2.2431159E-02 -7.4055768E-03 1,midg,midg; igrid,midg,midg 1.0544217E-02 -3.7197012E-02 gauss-seidel spectral radius is 0.9987206 estimated iterations to convergence 221 setup time was (sec) 1.020000 now iterating at: 16:27:38 rms-change max change #iterations 4.275259 172.9371 at 10iterations 2.050636 80.90001 at 20iterations 0.9827615 32.79481 at 30iterations 0.4717766 16.15585 at 40iterations 0.2270745 7.138222 at 50iterations 0.1087989 3.699636 at 60iterations 5.2191235E-02 1.658594 at 70iterations 2.5096644E-02 0.7978224 at 80iterations 1.2068423E-02 0.4217720 at 90iterations 5.8237272E-03 0.1784286 at 100iterations 2.7952767E-03 8.5098267E-02 at 110iterations 1.3537011E-03 4.0952682E-02 at 120iterations finished qdiffx linear iterations at : 16:27:50 total time elapsed so far: 13.36000 # loops : 120 mean,max change (kT/e) : 1.3537011E-03 4.0952682E-02 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 16:27:51 13.541u 0.494s 0:14.30 98.1% 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 Sat Oct 8 2011 at 16:27:51 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 = 2270 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: 3.000168 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): -2.119000 47.63600 ymin,ymax (A): -17.75300 28.83400 zmin,zma (A): -18.13700 35.26000 x,y,z range (A): 49.75500 46.58700 53.39700 scale (grids/A): 3.000168 object centre (A): 22.75850 5.540500 8.561502 number of atom coordinates read : 2270 total number of charged atoms : 2186 net assigned charge : 3.000000 assigned positive charge : 334.3273 centred at (gu) : 89.54671 86.74890 90.38710 assigned negative charge : -331.3279 centred at (gu) : 89.79527 87.37187 90.71956 start vw surface at 0.1100000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 165551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19272 grid for indexing accessible points = 1.400000 m= 84995 mr = 120916 m= 34584 mr = 69660 m= 10151 mr = 28414 m= 1667 mr = 8058 m= 99 mr = 1096 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 1350 time to turn everything in is 1.720000 number of dielectric boundary points 68867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 17488 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) : 2.000112 object centre at (A) : 22.75850 5.540500 8.561502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2808004 -3.6772739E-02 midg,1,midg; midg,igrid,midg 0.1475721 -9.7587459E-02 1,midg,midg; igrid,midg,midg 0.1334772 -0.4737141 gauss-seidel spectral radius is 0.9992736 estimated iterations to convergence 293 setup time was (sec) 2.110000 now iterating at: 16:27:53 rms-change max change #iterations 9.896900 375.7261 at 10iterations 5.822027 127.9436 at 20iterations 3.418064 71.78944 at 30iterations 2.005941 47.24902 at 40iterations 1.170223 22.78503 at 50iterations 0.6812786 12.25904 at 60iterations 0.3966370 7.569746 at 70iterations 0.2309405 4.221920 at 80iterations 0.1340406 2.684410 at 90iterations 7.7648155E-02 1.318883 at 100iterations 4.5038924E-02 0.7973766 at 110iterations 2.6125155E-02 0.4700661 at 120iterations 1.5139095E-02 0.2694759 at 130iterations 8.7612513E-03 0.1684430 at 140iterations 5.0783944E-03 9.1718674E-02 at 150iterations 2.9581075E-03 5.3236008E-02 at 160iterations 1.7240237E-03 3.2140732E-02 at 170iterations 1.0106310E-03 1.7776489E-02 at 180iterations finished qdiffx linear iterations at : 16:28:12 total time elapsed so far: 21.26000 # loops : 180 mean,max change (kT/e) : 1.0106310E-03 1.7776489E-02 energy calculations done at 21.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.42000 DelPhi exited at 16:28:13 21.426u 0.540s 0:22.27 98.6% 0+0k 0+0io 0pf+0w