Mon Oct 10 20:17:15 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 20:17:15 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 = 4285 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: 0.5513054 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): -3.387000 61.18000 ymin,ymax (A): -12.18800 38.37800 zmin,zma (A): -19.52700 45.04700 x,y,z range (A): 64.56700 50.56600 64.57401 scale (grids/A): 0.5513054 object centre (A): 28.89650 13.09500 12.76000 number of atom coordinates read : 4285 total number of charged atoms : 4132 net assigned charge : -4.499941 assigned positive charge : 643.4419 centred at (gu) : 89.18869 89.94042 90.75446 assigned negative charge : -647.9445 centred at (gu) : 89.22242 90.04969 90.78244 start vw surface at 0.2000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8216 nv = 96 ne = 84 npr = 90596 no. pairs analyzed = 90596 no. exposed pairs = 4890 no. arc points = 32364 no. surface atoms = 1670 nbur = 2615 mkacc time = 0.2500000 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= 368 mr = 4739 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.5100000 number of dielectric boundary points 3816 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3328 ## 402 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 10956 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6154755E-11 -8.1334006E-10 midg,1,midg; midg,igrid,midg 9.3982655E-10 -1.6270163E-09 1,midg,midg; igrid,midg,midg 6.6347851E-11 -6.1126504E-10 gauss-seidel spectral radius is 0.9831200 estimated iterations to convergence 63 setup time was (sec) 0.7900000 now iterating at: 20:17:16 rms-change max change #iterations 9.2763700E-02 13.89461 at 10iterations 6.9577005E-03 0.9805927 at 20iterations 1.0316388E-03 0.1285858 at 30iterations 3.4785055E-04 4.2453766E-02 at 40iterations 1.3041330E-04 1.6803741E-02 at 50iterations finished qdiffx linear iterations at : 20:17:19 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 1.3041330E-04 1.6803741E-02 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 20:17:20 4.262u 0.250s 0:05.19 86.8% 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 20:17:20 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 = 4285 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: 1.653916 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): -3.387000 61.18000 ymin,ymax (A): -12.18800 38.37800 zmin,zma (A): -19.52700 45.04700 x,y,z range (A): 64.56700 50.56600 64.57401 scale (grids/A): 1.653916 object centre (A): 28.89650 13.09500 12.76000 number of atom coordinates read : 4285 total number of charged atoms : 4132 net assigned charge : -4.499941 assigned positive charge : 643.4419 centred at (gu) : 87.56488 89.82002 92.26218 assigned negative charge : -647.9445 centred at (gu) : 87.66663 90.14886 92.34678 start vw surface at 0.2000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 92592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32364 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30428 mr = 67275 m= 3542 mr = 22016 m= 114 mr = 1921 m= 0 mr = 18 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1560 time to turn everything in is 0.8100000 number of dielectric boundary points 35446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 346 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 31810 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) : 0.5513054 object centre at (A) : 28.89650 13.09500 12.76000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2417228E-02 -1.3327575E-02 midg,1,midg; midg,igrid,midg 5.6115403E-03 -1.9210858E-02 1,midg,midg; igrid,midg,midg 1.6954510E-02 2.9377379E-02 gauss-seidel spectral radius is 0.9983474 estimated iterations to convergence 195 setup time was (sec) 1.120000 now iterating at: 20:17:22 rms-change max change #iterations 4.182938 179.4019 at 10iterations 1.817660 71.98926 at 20iterations 0.7900853 25.67106 at 30iterations 0.3428811 10.17209 at 40iterations 0.1493780 4.795841 at 50iterations 6.5258175E-02 2.012758 at 60iterations 2.8536616E-02 0.9473152 at 70iterations 1.2566682E-02 0.3654909 at 80iterations 5.5976817E-03 0.1987543 at 90iterations 2.5899224E-03 8.1544161E-02 at 100iterations 1.2763391E-03 3.7010193E-02 at 110iterations 6.9621427E-04 2.0559311E-02 at 120iterations finished qdiffx linear iterations at : 20:17:30 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 6.9621427E-04 2.0559311E-02 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.640000 DelPhi exited at 20:17:30 9.640u 0.291s 0:10.31 96.3% 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 Mon Oct 10 2011 at 20:17:31 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 = 4285 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: 2.480875 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): -3.387000 61.18000 ymin,ymax (A): -12.18800 38.37800 zmin,zma (A): -19.52700 45.04700 x,y,z range (A): 64.56700 50.56600 64.57401 scale (grids/A): 2.480875 object centre (A): 28.89650 13.09500 12.76000 number of atom coordinates read : 4285 total number of charged atoms : 4132 net assigned charge : -4.499941 assigned positive charge : 643.4419 centred at (gu) : 86.34695 89.72977 93.39291 assigned negative charge : -647.9445 centred at (gu) : 86.49983 90.22313 93.52000 start vw surface at 0.1900000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 215902 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32364 grid for indexing accessible points = 1.400000 m= 105374 mr = 164261 m= 31438 mr = 86051 m= 5785 mr = 24372 m= 487 mr = 4022 m= 7 mr = 248 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 5222 time to turn everything in is 2.000000 number of dielectric boundary points 80039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 33031 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) : 1.653916 object centre at (A) : 28.89650 13.09500 12.76000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5424942 -0.3009341 midg,1,midg; midg,igrid,midg 8.2603209E-02 -0.2536365 1,midg,midg; igrid,midg,midg 0.4118112 0.4823262 gauss-seidel spectral radius is 0.9992109 estimated iterations to convergence 281 setup time was (sec) 2.340000 now iterating at: 20:17:33 rms-change max change #iterations 10.78106 356.6622 at 10iterations 6.220891 144.4357 at 20iterations 3.579576 73.33439 at 30iterations 2.050879 36.59074 at 40iterations 1.170133 21.52405 at 50iterations 0.6666803 13.74995 at 60iterations 0.3794940 6.444908 at 70iterations 0.2153563 3.626220 at 80iterations 0.1218642 2.218360 at 90iterations 6.9279902E-02 1.192613 at 100iterations 3.9299935E-02 0.6572018 at 110iterations 2.2293206E-02 0.3945789 at 120iterations 1.2697102E-02 0.2253876 at 130iterations 7.2186459E-03 0.1217079 at 140iterations 4.1593644E-03 7.6408386E-02 at 150iterations 2.4394148E-03 4.1284561E-02 at 160iterations 1.4668613E-03 2.5241852E-02 at 170iterations 9.2322874E-04 1.5930176E-02 at 180iterations finished qdiffx linear iterations at : 20:17:47 total time elapsed so far: 16.21000 # loops : 180 mean,max change (kT/e) : 9.2322874E-04 1.5930176E-02 energy calculations done at 16.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.39000 DelPhi exited at 20:17:48 16.389u 0.313s 0:17.24 96.8% 0+0k 0+0io 0pf+0w