Thu Jan 19 13:31:43 PST 2012 #!/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 Thu Jan 19 2012 at 13:31:43 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6815 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4665365 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): -5.516000 70.79100 ymin,ymax (A): -0.4720000 75.65000 zmin,zma (A): 161.1640 229.0980 x,y,z range (A): 76.30700 76.12200 67.93399 scale (grids/A): 0.4665365 object centre (A): 32.63750 37.58900 195.1310 number of atom coordinates read : 6815 total number of charged atoms : 6645 net assigned charge : -0.7999669 assigned positive charge : 1034.981 centred at (gu) : 90.00414 89.96262 89.30226 assigned negative charge : -1035.789 centred at (gu) : 89.97471 90.03189 89.28447 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8961 nv = 96 ne = 84 npr = 139166 no. pairs analyzed = 139166 no. exposed pairs = 8893 no. arc points = 60047 no. surface atoms = 2979 nbur = 3836 mkacc time = 0.2400000 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 = 1.820000 m= 292 mr = 4407 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.4500000 number of dielectric boundary points 4844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5378 ## 926 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 12283 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2025613E-11 5.8997004E-12 midg,1,midg; midg,igrid,midg 3.1929587E-11 -3.4421556E-11 1,midg,midg; igrid,midg,midg -1.5413316E-11 1.2782415E-11 gauss-seidel spectral radius is 0.9766641 estimated iterations to convergence 54 setup time was (sec) 0.6500000 now iterating at: 13:31:44 rms-change max change #iterations 4.7909468E-02 11.10464 at 10iterations 3.3167836E-03 0.5211539 at 20iterations 1.1771265E-03 0.2055988 at 30iterations 5.3441734E-04 9.2123032E-02 at 40iterations 2.4289633E-04 4.1431427E-02 at 50iterations finished qdiffx linear iterations at : 13:31:49 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 2.4289633E-04 4.1431427E-02 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 13:31:50 3.731u 0.170s 0:07.40 52.7% 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 Thu Jan 19 2012 at 13:31:50 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6815 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.399609 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): -5.516000 70.79100 ymin,ymax (A): -0.4720000 75.65000 zmin,zma (A): 161.1640 229.0980 x,y,z range (A): 76.30700 76.12200 67.93399 scale (grids/A): 1.399609 object centre (A): 32.63750 37.58900 195.1310 number of atom coordinates read : 6815 total number of charged atoms : 6645 net assigned charge : -0.7999669 assigned positive charge : 1034.981 centred at (gu) : 90.01080 89.88583 87.90471 assigned negative charge : -1035.789 centred at (gu) : 89.92370 90.09570 87.85284 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 103395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60047 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 26633 mr = 69574 m= 1739 mr = 16407 m= 21 mr = 534 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 399 time to turn everything in is 0.5300000 number of dielectric boundary points 45273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 957 ## 27 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 47870 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) : 0.4665365 object centre at (A) : 32.63750 37.58900 195.1310 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3194521E-03 -1.4593950E-03 midg,1,midg; midg,igrid,midg 3.0614038E-03 -8.1369383E-03 1,midg,midg; igrid,midg,midg 1.6917846E-03 1.6753990E-02 gauss-seidel spectral radius is 0.9978679 estimated iterations to convergence 172 setup time was (sec) 0.7500000 now iterating at: 13:31:51 rms-change max change #iterations 3.839649 180.0253 at 10iterations 1.483989 50.41824 at 20iterations 0.5756292 19.56807 at 30iterations 0.2236410 7.262100 at 40iterations 8.6555175E-02 2.605373 at 50iterations 3.3925828E-02 0.9952335 at 60iterations 1.3340910E-02 0.4632626 at 70iterations 5.3854161E-03 0.1714321 at 80iterations 2.3615565E-03 7.6943398E-02 at 90iterations 1.2158889E-03 4.4679642E-02 at 100iterations 7.5378350E-04 2.8179169E-02 at 110iterations 5.2206102E-04 1.6774178E-02 at 120iterations finished qdiffx linear iterations at : 13:32:05 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 5.2206102E-04 1.6774178E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 13:32:06 8.134u 0.217s 0:15.50 53.8% 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 Thu Jan 19 2012 at 13:32:06 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6815 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.099414 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): -5.516000 70.79100 ymin,ymax (A): -0.4720000 75.65000 zmin,zma (A): 161.1640 229.0980 x,y,z range (A): 76.30700 76.12200 67.93399 scale (grids/A): 2.099414 object centre (A): 32.63750 37.58900 195.1310 number of atom coordinates read : 6815 total number of charged atoms : 6645 net assigned charge : -0.7999669 assigned positive charge : 1034.981 centred at (gu) : 90.01584 89.82841 86.85641 assigned negative charge : -1035.789 centred at (gu) : 89.88555 90.14341 86.77908 start vw surface at 0.1700000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 242464 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60047 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 99462 mr = 172935 m= 20866 mr = 74674 m= 2186 mr = 13856 m= 52 mr = 1102 m= 0 mr = 3 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 1219 time to turn everything in is 1.250000 number of dielectric boundary points 102460 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 216 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 52556 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) : 1.399609 object centre at (A) : 32.63750 37.58900 195.1310 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4802969E-02 -4.3821678E-02 midg,1,midg; midg,igrid,midg 4.6900619E-02 -6.4507961E-02 1,midg,midg; igrid,midg,midg 0.1558303 0.4816879 gauss-seidel spectral radius is 0.9991283 estimated iterations to convergence 268 setup time was (sec) 1.520000 now iterating at: 13:32:08 rms-change max change #iterations 11.06260 298.4130 at 10iterations 6.257212 148.0602 at 20iterations 3.512179 78.47620 at 30iterations 1.968414 46.32862 at 40iterations 1.095412 23.94342 at 50iterations 0.6083137 11.90852 at 60iterations 0.3366422 7.020776 at 70iterations 0.1862768 3.554230 at 80iterations 0.1028927 2.057327 at 90iterations 5.6814913E-02 1.123637 at 100iterations 3.1357735E-02 0.6212792 at 110iterations 1.7245369E-02 0.3454399 at 120iterations 9.5244134E-03 0.2084942 at 130iterations 5.2837832E-03 0.1162891 at 140iterations 2.9542060E-03 5.6684494E-02 at 150iterations 1.6796798E-03 3.3689499E-02 at 160iterations 9.8692486E-04 2.3384094E-02 at 170iterations 6.1211007E-04 1.1367798E-02 at 180iterations finished qdiffx linear iterations at : 13:32:33 total time elapsed so far: 14.42000 # loops : 180 mean,max change (kT/e) : 6.1211007E-04 1.1367798E-02 energy calculations done at 14.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.54000 DelPhi exited at 13:32:33 14.541u 0.270s 0:26.97 54.9% 0+0k 0+0io 0pf+0w