Mon Oct 10 14:16:55 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 14:16:55 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 !!! WARNING: ADP 667 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5889555 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): -35.30500 25.14100 ymin,ymax (A): -15.72100 34.76500 zmin,zma (A): -2.105000 52.72400 x,y,z range (A): 60.44600 50.48600 54.82900 scale (grids/A): 0.5889555 object centre (A): -5.082001 9.522001 25.30950 number of atom coordinates read : 2493 total number of charged atoms : 2371 net assigned charge : -5.999993 assigned positive charge : 384.3789 centred at (gu) : 92.84319 89.88167 89.26945 assigned negative charge : -390.3795 centred at (gu) : 92.84966 89.94677 89.39677 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5924 nv = 96 ne = 84 npr = 47841 no. pairs analyzed = 47841 no. exposed pairs = 3522 no. arc points = 24725 no. surface atoms = 1189 nbur = 1304 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 = 1.456000 m= 267 mr = 2915 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3263 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2493 ## 275 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7310 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7177206E-09 -4.3097299E-09 midg,1,midg; midg,igrid,midg -1.2999253E-10 -3.3742285E-09 1,midg,midg; igrid,midg,midg -8.6971336E-10 -3.7343164E-09 gauss-seidel spectral radius is 0.9850845 estimated iterations to convergence 67 setup time was (sec) 0.5000000 now iterating at: 14:16:55 rms-change max change #iterations 9.7402275E-02 17.45628 at 10iterations 8.0164354E-03 1.368871 at 20iterations 6.9145585E-04 0.1071405 at 30iterations 8.9091343E-05 1.6353607E-02 at 40iterations 2.0678903E-05 4.1389465E-03 at 50iterations finished qdiffx linear iterations at : 14:16:58 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 2.0678903E-05 4.1389465E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 14:16:58 3.097u 0.154s 0:03.62 89.5% 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 14:16:58 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 !!! WARNING: ADP 667 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.766866 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): -35.30500 25.14100 ymin,ymax (A): -15.72100 34.76500 zmin,zma (A): -2.105000 52.72400 x,y,z range (A): 60.44600 50.48600 54.82900 scale (grids/A): 1.766866 object centre (A): -5.082001 9.522001 25.30950 number of atom coordinates read : 2493 total number of charged atoms : 2371 net assigned charge : -5.999993 assigned positive charge : 384.3789 centred at (gu) : 98.52916 89.64455 87.80743 assigned negative charge : -390.3795 centred at (gu) : 98.54872 89.84012 88.18999 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 64230 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24725 grid for indexing accessible points = 1.400000 m= 21246 mr = 42328 m= 2795 mr = 14409 m= 100 mr = 1400 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 30215 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 225 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 18467 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) : 0.5889555 object centre at (A) : -5.082001 9.522001 25.30950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9818292E-03 -2.2114296E-02 midg,1,midg; midg,igrid,midg -5.7965382E-03 -1.1274724E-02 1,midg,midg; igrid,midg,midg 1.7177742E-02 4.8317378E-03 gauss-seidel spectral radius is 0.9984204 estimated iterations to convergence 200 setup time was (sec) 0.7200000 now iterating at: 14:16:59 rms-change max change #iterations 3.680676 183.1241 at 10iterations 1.621845 74.57364 at 20iterations 0.7169465 27.13907 at 30iterations 0.3164970 10.96682 at 40iterations 0.1399633 5.381008 at 50iterations 6.1854500E-02 2.294746 at 60iterations 2.7395746E-02 1.002174 at 70iterations 1.2102931E-02 0.4171200 at 80iterations 5.3320001E-03 0.2171707 at 90iterations 2.3710451E-03 8.9241028E-02 at 100iterations 1.0435920E-03 3.5129547E-02 at 110iterations 4.6193250E-04 1.7717361E-02 at 120iterations finished qdiffx linear iterations at : 14:17:05 total time elapsed so far: 6.590000 # loops : 120 mean,max change (kT/e) : 4.6193250E-04 1.7717361E-02 energy calculations done at 6.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.760000 DelPhi exited at 14:17:06 6.763u 0.165s 0:07.35 94.1% 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 14:17:06 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 !!! WARNING: ADP 667 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.650300 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): -35.30500 25.14100 ymin,ymax (A): -15.72100 34.76500 zmin,zma (A): -2.105000 52.72400 x,y,z range (A): 60.44600 50.48600 54.82900 scale (grids/A): 2.650300 object centre (A): -5.082001 9.522001 25.30950 number of atom coordinates read : 2493 total number of charged atoms : 2371 net assigned charge : -5.999993 assigned positive charge : 384.3789 centred at (gu) : 102.7935 89.46661 86.71109 assigned negative charge : -390.3795 centred at (gu) : 102.8231 89.76015 87.28503 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 148620 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24725 grid for indexing accessible points = 1.400000 m= 70638 mr = 103798 m= 22911 mr = 54987 m= 4587 mr = 16997 m= 508 mr = 3030 m= 16 mr = 276 m= 0 mr = 2 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 68190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 18965 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) : 1.766866 object centre at (A) : -5.082001 9.522001 25.30950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1698420E-02 -0.2255950 midg,1,midg; midg,igrid,midg -8.0314957E-02 -8.2895473E-02 1,midg,midg; igrid,midg,midg 0.4159857 -9.8172752E-03 gauss-seidel spectral radius is 0.9992073 estimated iterations to convergence 280 setup time was (sec) 1.370000 now iterating at: 14:17:07 rms-change max change #iterations 9.183448 300.5037 at 10iterations 5.347345 159.0798 at 20iterations 3.074376 77.22267 at 30iterations 1.759355 40.42967 at 40iterations 1.002326 23.07643 at 50iterations 0.5696059 12.73416 at 60iterations 0.3231714 6.739899 at 70iterations 0.1827660 4.482674 at 80iterations 0.1032029 2.520484 at 90iterations 5.8390040E-02 1.213333 at 100iterations 3.2985520E-02 0.6978607 at 110iterations 1.8616496E-02 0.4438477 at 120iterations 1.0484757E-02 0.2258134 at 130iterations 5.9290784E-03 0.1191254 at 140iterations 3.3448804E-03 6.9610596E-02 at 150iterations 1.8844904E-03 4.1213989E-02 at 160iterations 1.0670871E-03 3.0429840E-02 at 170iterations 6.0690078E-04 1.3172150E-02 at 180iterations finished qdiffx linear iterations at : 14:17:17 total time elapsed so far: 10.70000 # loops : 180 mean,max change (kT/e) : 6.0690078E-04 1.3172150E-02 energy calculations done at 10.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.87000 DelPhi exited at 14:17:17 10.875u 0.176s 0:11.40 96.8% 0+0k 0+0io 0pf+0w