Tue Oct 11 08:16:18 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 08:16:18 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: FMN 398 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6632264 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): -24.93300 21.51800 ymin,ymax (A): -64.18200 -10.50500 zmin,zma (A): -17.28900 29.93100 x,y,z range (A): 46.45100 53.67700 47.22000 scale (grids/A): 0.6632264 object centre (A): -1.707500 -37.34350 6.321000 number of atom coordinates read : 2741 total number of charged atoms : 2606 net assigned charge : 3.000016 assigned positive charge : 419.6884 centred at (gu) : 90.70654 89.93385 90.60629 assigned negative charge : -416.6894 centred at (gu) : 90.54951 90.20140 90.65487 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8177 nv = 96 ne = 84 npr = 56655 no. pairs analyzed = 56655 no. exposed pairs = 3376 no. arc points = 22912 no. surface atoms = 1136 nbur = 1605 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 4706 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2100000 number of dielectric boundary points 3880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2110 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9532 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7063227E-08 -3.5700676E-09 midg,1,midg; midg,igrid,midg 6.9119189E-08 -5.4517923E-08 1,midg,midg; igrid,midg,midg -2.4614007E-08 5.0806513E-08 gauss-seidel spectral radius is 0.9882284 estimated iterations to convergence 75 setup time was (sec) 0.4000000 now iterating at: 08:16:19 rms-change max change #iterations 0.1802738 27.67284 at 10iterations 1.9988334E-02 2.761810 at 20iterations 3.1679806E-03 0.6069336 at 30iterations 9.3517505E-04 0.1924820 at 40iterations 3.4188954E-04 7.0884705E-02 at 50iterations finished qdiffx linear iterations at : 08:16:22 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 3.4188954E-04 7.0884705E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 08:16:22 3.346u 0.163s 0:03.92 89.2% 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 08:16:22 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: FMN 398 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.989679 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): -24.93300 21.51800 ymin,ymax (A): -64.18200 -10.50500 zmin,zma (A): -17.28900 29.93100 x,y,z range (A): 46.45100 53.67700 47.22000 scale (grids/A): 1.989679 object centre (A): -1.707500 -37.34350 6.321000 number of atom coordinates read : 2741 total number of charged atoms : 2606 net assigned charge : 3.000016 assigned positive charge : 419.6884 centred at (gu) : 92.11886 89.80079 91.81780 assigned negative charge : -416.6894 centred at (gu) : 91.64806 90.60410 91.96430 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 88244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22912 grid for indexing accessible points = 1.400000 m= 33393 mr = 62974 m= 5800 mr = 25154 m= 438 mr = 3792 m= 4 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1440 time to turn everything in is 0.4100000 number of dielectric boundary points 35778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20588 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) : 0.6632264 object centre at (A) : -1.707500 -37.34350 6.321000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7128740E-02 -2.7655490E-02 midg,1,midg; midg,igrid,midg 7.4164614E-02 -6.1093528E-02 1,midg,midg; igrid,midg,midg -1.6523981E-02 5.2961364E-02 gauss-seidel spectral radius is 0.9987603 estimated iterations to convergence 225 setup time was (sec) 0.6400000 now iterating at: 08:16:23 rms-change max change #iterations 4.820313 286.3796 at 10iterations 2.348062 68.81531 at 20iterations 1.135983 35.26594 at 30iterations 0.5509952 16.27787 at 40iterations 0.2687116 7.928476 at 50iterations 0.1301917 3.559966 at 60iterations 6.3634835E-02 1.814510 at 70iterations 3.1211892E-02 1.015602 at 80iterations 1.5473178E-02 0.4367943 at 90iterations 7.8670876E-03 0.2458801 at 100iterations 4.1763401E-03 0.1352234 at 110iterations 2.3662653E-03 9.2605591E-02 at 120iterations finished qdiffx linear iterations at : 08:16:30 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 2.3662653E-03 9.2605591E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 08:16:31 7.768u 0.192s 0:08.58 92.6% 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 08:16:31 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 2.984519 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): -24.93300 21.51800 ymin,ymax (A): -64.18200 -10.50500 zmin,zma (A): -17.28900 29.93100 x,y,z range (A): 46.45100 53.67700 47.22000 scale (grids/A): 2.984519 object centre (A): -1.707500 -37.34350 6.321000 number of atom coordinates read : 2741 total number of charged atoms : 2606 net assigned charge : 3.000016 assigned positive charge : 419.6884 centred at (gu) : 93.17825 89.70107 92.72655 assigned negative charge : -416.6894 centred at (gu) : 92.47208 90.90608 92.94625 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 203836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22912 grid for indexing accessible points = 1.400000 m= 106531 mr = 151839 m= 40820 mr = 88450 m= 10585 mr = 33443 m= 1790 mr = 8115 m= 150 mr = 1222 m= 6 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 5019 time to turn everything in is 1.110000 number of dielectric boundary points 80573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 20848 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) : 1.989679 object centre at (A) : -1.707500 -37.34350 6.321000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2335940 -0.3097364 midg,1,midg; midg,igrid,midg 0.9753106 -0.6718419 1,midg,midg; igrid,midg,midg -0.1694611 0.4281354 gauss-seidel spectral radius is 0.9992905 estimated iterations to convergence 296 setup time was (sec) 1.350000 now iterating at: 08:16:32 rms-change max change #iterations 11.13009 349.1825 at 10iterations 6.557067 151.3444 at 20iterations 3.866237 86.20141 at 30iterations 2.272611 42.01364 at 40iterations 1.332346 23.42967 at 50iterations 0.7800933 15.11794 at 60iterations 0.4565927 7.455477 at 70iterations 0.2664486 4.748487 at 80iterations 0.1557297 2.570129 at 90iterations 9.0844393E-02 1.475066 at 100iterations 5.3094357E-02 0.9290104 at 110iterations 3.1091940E-02 0.5568619 at 120iterations 1.8356247E-02 0.3420868 at 130iterations 1.0953120E-02 0.2194862 at 140iterations 6.6826693E-03 0.1418228 at 150iterations 4.2265574E-03 9.8705292E-02 at 160iterations 2.8274767E-03 6.8019867E-02 at 170iterations 2.0209136E-03 5.0018311E-02 at 180iterations finished qdiffx linear iterations at : 08:16:44 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 2.0209136E-03 5.0018311E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 08:16:44 12.762u 0.194s 0:13.53 95.7% 0+0k 0+0io 0pf+0w