Tue Oct 11 06:15:48 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 06:15:48 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 = 2007 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: 0.7318778 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): -19.51600 23.73700 ymin,ymax (A): -10.98900 27.42500 zmin,zma (A): -2.923000 45.71900 x,y,z range (A): 43.25300 38.41400 48.64200 scale (grids/A): 0.7318778 object centre (A): 2.110500 8.218000 21.39800 number of atom coordinates read : 2007 total number of charged atoms : 1892 net assigned charge : 7.500010 assigned positive charge : 306.7150 centred at (gu) : 89.83217 89.25920 91.14465 assigned negative charge : -299.2151 centred at (gu) : 89.65714 89.27450 91.25204 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7524 nv = 96 ne = 84 npr = 39293 no. pairs analyzed = 39293 no. exposed pairs = 2566 no. arc points = 17787 no. surface atoms = 864 nbur = 1143 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 542 mr = 4292 m= 8 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1597 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7967 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5939037E-07 2.9258652E-08 midg,1,midg; midg,igrid,midg 1.4234399E-07 8.7227846E-08 1,midg,midg; igrid,midg,midg -3.2057230E-08 2.4215862E-07 gauss-seidel spectral radius is 0.9902591 estimated iterations to convergence 82 setup time was (sec) 0.4800000 now iterating at: 06:15:49 rms-change max change #iterations 0.2251226 32.97015 at 10iterations 2.9220153E-02 4.347339 at 20iterations 3.9546830E-03 0.4878712 at 30iterations 5.9553713E-04 7.6019287E-02 at 40iterations 1.1964843E-04 1.5487671E-02 at 50iterations finished qdiffx linear iterations at : 06:15:52 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 1.1964843E-04 1.5487671E-02 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 06:15:52 3.277u 0.166s 0:03.84 89.3% 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 06:15:52 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 = 2007 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.195633 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): -19.51600 23.73700 ymin,ymax (A): -10.98900 27.42500 zmin,zma (A): -2.923000 45.71900 x,y,z range (A): 43.25300 38.41400 48.64200 scale (grids/A): 2.195633 object centre (A): 2.110500 8.218000 21.39800 number of atom coordinates read : 2007 total number of charged atoms : 1892 net assigned charge : 7.500010 assigned positive charge : 306.7150 centred at (gu) : 89.49642 87.77779 93.43407 assigned negative charge : -299.2151 centred at (gu) : 88.97144 87.82336 93.75622 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78645 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17787 grid for indexing accessible points = 1.400000 m= 33759 mr = 55369 m= 7433 mr = 25887 m= 773 mr = 5065 m= 21 mr = 395 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 33913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 15064 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) : 0.7318778 object centre at (A) : 2.110500 8.218000 21.39800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2169753E-02 6.4269886E-03 midg,1,midg; midg,igrid,midg 4.5867752E-02 2.3106022E-02 1,midg,midg; igrid,midg,midg 2.6302056E-02 5.5523537E-02 gauss-seidel spectral radius is 0.9988959 estimated iterations to convergence 238 setup time was (sec) 0.8800000 now iterating at: 06:15:53 rms-change max change #iterations 4.795566 207.7667 at 10iterations 2.416094 83.11797 at 20iterations 1.230412 35.95764 at 30iterations 0.6255918 18.89647 at 40iterations 0.3160289 9.939329 at 50iterations 0.1603835 4.881190 at 60iterations 8.0935054E-02 2.259268 at 70iterations 4.1075960E-02 1.235820 at 80iterations 2.0794099E-02 0.6626165 at 90iterations 1.0536961E-02 0.2925720 at 100iterations 5.3862911E-03 0.1737261 at 110iterations 2.7618599E-03 8.4522724E-02 at 120iterations finished qdiffx linear iterations at : 06:16:00 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 2.7618599E-03 8.4522724E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 06:16:00 7.530u 0.228s 0:08.09 95.7% 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 06:16:01 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 = 2007 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.293450 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): -19.51600 23.73700 ymin,ymax (A): -10.98900 27.42500 zmin,zma (A): -2.923000 45.71900 x,y,z range (A): 43.25300 38.41400 48.64200 scale (grids/A): 3.293450 object centre (A): 2.110500 8.218000 21.39800 number of atom coordinates read : 2007 total number of charged atoms : 1892 net assigned charge : 7.500010 assigned positive charge : 306.7150 centred at (gu) : 89.24467 86.66668 95.15118 assigned negative charge : -299.2151 centred at (gu) : 88.45723 86.73515 95.63448 start vw surface at 0.1400000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 180633 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17787 grid for indexing accessible points = 1.400000 m= 102311 mr = 133047 m= 45288 mr = 85437 m= 14290 mr = 37378 m= 3095 mr = 11160 m= 384 mr = 2274 m= 13 mr = 248 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.910000 number of dielectric boundary points 76468 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 15136 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) : 2.195633 object centre at (A) : 2.110500 8.218000 21.39800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1901378 -3.7796309E-03 midg,1,midg; midg,igrid,midg 0.3563806 0.1573719 1,midg,midg; igrid,midg,midg 0.4865555 0.4312517 gauss-seidel spectral radius is 0.9993139 estimated iterations to convergence 301 setup time was (sec) 2.200000 now iterating at: 06:16:03 rms-change max change #iterations 10.62109 345.0122 at 10iterations 6.378661 129.1628 at 20iterations 3.816652 75.48454 at 30iterations 2.275980 43.92110 at 40iterations 1.354067 25.57385 at 50iterations 0.8029644 14.31131 at 60iterations 0.4754497 8.566612 at 70iterations 0.2820962 4.573715 at 80iterations 0.1669371 2.997135 at 90iterations 9.8435752E-02 1.846655 at 100iterations 5.8228366E-02 1.072021 at 110iterations 3.4394290E-02 0.6154327 at 120iterations 2.0442169E-02 0.3627737 at 130iterations 1.2231450E-02 0.2216988 at 140iterations 7.3946631E-03 0.1402512 at 150iterations 4.5761019E-03 8.4707260E-02 at 160iterations 2.9429917E-03 5.1158905E-02 at 170iterations 1.9981032E-03 3.3058167E-02 at 180iterations finished qdiffx linear iterations at : 06:16:13 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 1.9981032E-03 3.3058167E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 06:16:14 12.706u 0.277s 0:13.35 97.1% 0+0k 0+0io 0pf+0w