Tue Oct 11 08:22:00 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 08:22:00 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 = 3424 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5418487 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): 46.20700 101.9450 ymin,ymax (A): -1.297000 60.72400 zmin,zma (A): 56.52800 122.2290 x,y,z range (A): 55.73800 62.02100 65.70100 scale (grids/A): 0.5418487 object centre (A): 74.07600 29.71350 89.37850 number of atom coordinates read : 3424 total number of charged atoms : 3271 net assigned charge : 3.500022 assigned positive charge : 529.6384 centred at (gu) : 88.94978 89.87360 88.16833 assigned negative charge : -526.1401 centred at (gu) : 88.98260 89.97714 88.24088 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6498 nv = 96 ne = 84 npr = 65923 no. pairs analyzed = 65923 no. exposed pairs = 4893 no. arc points = 34495 no. surface atoms = 1627 nbur = 1797 mkacc time = 0.1100000 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 = 1.596000 m= 276 mr = 2985 m= 0 mr = 4 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3501 ## 480 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8620 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0375254E-09 -1.9916023E-10 midg,1,midg; midg,igrid,midg 8.8337454E-10 -5.1459703E-10 1,midg,midg; igrid,midg,midg 5.0704591E-10 -3.6330251E-11 gauss-seidel spectral radius is 0.9824868 estimated iterations to convergence 62 setup time was (sec) 0.4500000 now iterating at: 08:22:01 rms-change max change #iterations 7.8254662E-02 12.12958 at 10iterations 5.0777732E-03 0.8577995 at 20iterations 3.4417087E-04 5.3798676E-02 at 30iterations 3.2744174E-05 5.7239532E-03 at 40iterations 7.1999007E-06 1.4553070E-03 at 50iterations finished qdiffx linear iterations at : 08:22:04 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 7.1999007E-06 1.4553070E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 08:22:04 3.557u 0.220s 0:04.19 89.9% 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 Tue Oct 11 2011 at 08:22:04 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 = 3424 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.625546 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): 46.20700 101.9450 ymin,ymax (A): -1.297000 60.72400 zmin,zma (A): 56.52800 122.2290 x,y,z range (A): 55.73800 62.02100 65.70100 scale (grids/A): 1.625546 object centre (A): 74.07600 29.71350 89.37850 number of atom coordinates read : 3424 total number of charged atoms : 3271 net assigned charge : 3.500022 assigned positive charge : 529.6384 centred at (gu) : 86.84830 89.62006 84.50428 assigned negative charge : -526.1401 centred at (gu) : 86.94738 89.93102 84.72211 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71108 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34495 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21413 mr = 44676 m= 2294 mr = 13863 m= 54 mr = 1085 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 282 time to turn everything in is 0.3600000 number of dielectric boundary points 35243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 390 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 24988 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) : 0.5418487 object centre at (A) : 74.07600 29.71350 89.37850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1515811E-02 -2.4696544E-04 midg,1,midg; midg,igrid,midg -3.3148883E-03 -1.1823559E-02 1,midg,midg; igrid,midg,midg 1.0731171E-02 3.0681875E-03 gauss-seidel spectral radius is 0.9982295 estimated iterations to convergence 189 setup time was (sec) 0.5800000 now iterating at: 08:22:05 rms-change max change #iterations 3.649831 191.2439 at 10iterations 1.519581 59.78197 at 20iterations 0.6403225 23.62617 at 30iterations 0.2688338 9.980867 at 40iterations 0.1127979 4.326919 at 50iterations 4.7489308E-02 1.549768 at 60iterations 1.9869013E-02 0.6988888 at 70iterations 8.3788456E-03 0.3030891 at 80iterations 3.5296837E-03 0.1304913 at 90iterations 1.4825601E-03 4.8925400E-02 at 100iterations 6.2622980E-04 2.2727966E-02 at 110iterations 2.6335617E-04 8.6517334E-03 at 120iterations finished qdiffx linear iterations at : 08:22:12 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 2.6335617E-04 8.6517334E-03 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 08:22:13 8.161u 0.197s 0:08.86 94.2% 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 08:22:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3424 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: 2.438319 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): 46.20700 101.9450 ymin,ymax (A): -1.297000 60.72400 zmin,zma (A): 56.52800 122.2290 x,y,z range (A): 55.73800 62.02100 65.70100 scale (grids/A): 2.438319 object centre (A): 74.07600 29.71350 89.37850 number of atom coordinates read : 3424 total number of charged atoms : 3271 net assigned charge : 3.500022 assigned positive charge : 529.6384 centred at (gu) : 85.27222 89.42970 81.75619 assigned negative charge : -526.1401 centred at (gu) : 85.42086 89.89648 82.08308 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 164871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34495 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 73225 mr = 110219 m= 21037 mr = 55582 m= 3477 mr = 15263 m= 269 mr = 2139 m= 5 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 884 time to turn everything in is 0.8700000 number of dielectric boundary points 79559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 26142 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) : 1.625546 object centre at (A) : 74.07600 29.71350 89.37850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2036354E-03 5.6880381E-02 midg,1,midg; midg,igrid,midg -7.2954193E-02 -0.1798389 1,midg,midg; igrid,midg,midg 0.1572335 6.0448945E-02 gauss-seidel spectral radius is 0.9991705 estimated iterations to convergence 274 setup time was (sec) 1.120000 now iterating at: 08:22:14 rms-change max change #iterations 9.497380 326.7688 at 10iterations 5.458120 175.2515 at 20iterations 3.103546 79.79527 at 30iterations 1.756846 47.87809 at 40iterations 0.9912667 27.01505 at 50iterations 0.5573268 12.47238 at 60iterations 0.3129155 8.598787 at 70iterations 0.1750863 3.692511 at 80iterations 9.8007709E-02 2.207294 at 90iterations 5.4656900E-02 1.148174 at 100iterations 3.0522373E-02 0.6352196 at 110iterations 1.6959634E-02 0.3750105 at 120iterations 9.4887046E-03 0.2009392 at 130iterations 5.2726478E-03 0.1099777 at 140iterations 2.9352834E-03 5.7786226E-02 at 150iterations 1.6344590E-03 3.7677765E-02 at 160iterations 9.0865756E-04 1.8272400E-02 at 170iterations 5.0601619E-04 1.0623217E-02 at 180iterations finished qdiffx linear iterations at : 08:22:28 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 5.0601619E-04 1.0623217E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 08:22:29 12.930u 0.203s 0:15.60 84.1% 0+0k 0+0io 0pf+0w