Mon Oct 10 13:52:55 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 13:52:55 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 = 4406 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: 0.5027894 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): -3.495000 67.31000 ymin,ymax (A): -12.61800 38.32500 zmin,zma (A): -19.70400 45.31700 x,y,z range (A): 70.80500 50.94300 65.02100 scale (grids/A): 0.5027894 object centre (A): 31.90750 12.85350 12.80650 number of atom coordinates read : 4406 total number of charged atoms : 4251 net assigned charge : -5.499952 assigned positive charge : 664.2267 centred at (gu) : 88.10473 89.90237 90.79865 assigned negative charge : -669.7291 centred at (gu) : 88.15535 90.00960 90.81811 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6893 nv = 96 ne = 84 npr = 92574 no. pairs analyzed = 92574 no. exposed pairs = 5054 no. arc points = 33675 no. surface atoms = 1732 nbur = 2674 mkacc time = 0.1600000 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 = 1.680000 m= 242 mr = 3849 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3395 ## 516 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 9365 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8691829E-11 -1.1102815E-10 midg,1,midg; midg,igrid,midg 1.2952875E-10 -2.3746408E-10 1,midg,midg; igrid,midg,midg 5.3434146E-11 -8.7334535E-11 gauss-seidel spectral radius is 0.9797359 estimated iterations to convergence 58 setup time was (sec) 0.5000000 now iterating at: 13:52:56 rms-change max change #iterations 5.8689840E-02 9.507658 at 10iterations 3.6676675E-03 0.5387816 at 20iterations 5.5840390E-04 8.2714081E-02 at 30iterations 1.5501579E-04 2.4024963E-02 at 40iterations 4.5624969E-05 7.2898865E-03 at 50iterations finished qdiffx linear iterations at : 13:52:59 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 4.5624969E-05 7.2898865E-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 13:52:59 3.558u 0.185s 0:04.12 90.5% 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 13:52:59 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 = 4406 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: 1.508368 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): -3.495000 67.31000 ymin,ymax (A): -12.61800 38.32500 zmin,zma (A): -19.70400 45.31700 x,y,z range (A): 70.80500 50.94300 65.02100 scale (grids/A): 1.508368 object centre (A): 31.90750 12.85350 12.80650 number of atom coordinates read : 4406 total number of charged atoms : 4251 net assigned charge : -5.499952 assigned positive charge : 664.2267 centred at (gu) : 84.31309 89.70601 92.39476 assigned negative charge : -669.7291 centred at (gu) : 84.46533 90.02850 92.45395 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 78913 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33675 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23257 mr = 56652 m= 1925 mr = 16052 m= 29 mr = 854 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 575 time to turn everything in is 0.3900000 number of dielectric boundary points 30566 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 501 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 31852 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) : 0.5027894 object centre at (A) : 31.90750 12.85350 12.80650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9833539E-03 -7.8490097E-03 midg,1,midg; midg,igrid,midg 2.2472586E-03 -9.9035837E-03 1,midg,midg; igrid,midg,midg 6.5867128E-03 -4.6025733E-03 gauss-seidel spectral radius is 0.9979865 estimated iterations to convergence 177 setup time was (sec) 0.6000000 now iterating at: 13:53:00 rms-change max change #iterations 3.475386 168.7986 at 10iterations 1.381835 55.92181 at 20iterations 0.5496265 18.13204 at 30iterations 0.2203226 7.666512 at 40iterations 8.7790862E-02 3.070812 at 50iterations 3.5159741E-02 1.160755 at 60iterations 1.4178557E-02 0.4755402 at 70iterations 5.7495530E-03 0.1943836 at 80iterations 2.4103955E-03 8.1497192E-02 at 90iterations 1.0662228E-03 3.5284042E-02 at 100iterations 5.2013708E-04 1.9832611E-02 at 110iterations 2.8449591E-04 1.0253906E-02 at 120iterations finished qdiffx linear iterations at : 13:53:07 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 2.8449591E-04 1.0253906E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 13:53:08 7.908u 0.206s 0:08.51 95.1% 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 Mon Oct 10 2011 at 13:53:08 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 = 4406 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: 2.262552 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): -3.495000 67.31000 ymin,ymax (A): -12.61800 38.32500 zmin,zma (A): -19.70400 45.31700 x,y,z range (A): 70.80500 50.94300 65.02100 scale (grids/A): 2.262552 object centre (A): 31.90750 12.85350 12.80650 number of atom coordinates read : 4406 total number of charged atoms : 4251 net assigned charge : -5.499952 assigned positive charge : 664.2267 centred at (gu) : 81.46916 89.55885 93.59194 assigned negative charge : -669.7291 centred at (gu) : 81.69799 90.04251 93.68082 start vw surface at 0.1200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 184508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33675 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 84368 mr = 138773 m= 21030 mr = 67614 m= 2777 mr = 15569 m= 108 mr = 1733 m= 4 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 2132 time to turn everything in is 0.9500000 number of dielectric boundary points 69082 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 33890 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) : 1.508368 object centre at (A) : 31.90750 12.85350 12.80650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2407732 -0.1841761 midg,1,midg; midg,igrid,midg 2.4302967E-02 -0.1602833 1,midg,midg; igrid,midg,midg 0.1783741 -0.3874190 gauss-seidel spectral radius is 0.9990988 estimated iterations to convergence 263 setup time was (sec) 1.170000 now iterating at: 13:53:09 rms-change max change #iterations 9.478118 243.1373 at 10iterations 5.295328 174.9922 at 20iterations 2.937774 69.02959 at 30iterations 1.619453 33.62434 at 40iterations 0.8886855 20.49147 at 50iterations 0.4871516 9.763466 at 60iterations 0.2664284 5.440437 at 70iterations 0.1454596 3.044420 at 80iterations 7.9300851E-02 1.808485 at 90iterations 4.3196965E-02 0.9417133 at 100iterations 2.3519518E-02 0.4805658 at 110iterations 1.2807334E-02 0.2507915 at 120iterations 6.9965804E-03 0.1455412 at 130iterations 3.8314976E-03 9.3723297E-02 at 140iterations 2.1113846E-03 4.3585300E-02 at 150iterations 1.1820348E-03 2.3427963E-02 at 160iterations 6.7574176E-04 1.3639927E-02 at 170iterations 4.0150021E-04 8.7585449E-03 at 180iterations finished qdiffx linear iterations at : 13:53:21 total time elapsed so far: 12.45000 # loops : 180 mean,max change (kT/e) : 4.0150021E-04 8.7585449E-03 energy calculations done at 12.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 13:53:21 12.574u 0.237s 0:13.31 96.1% 0+0k 0+0io 0pf+0w