Wed Dec 21 14:20:39 PST 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 Wed Dec 21 2011 at 14:20:39 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5941751 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): -35.17700 11.30000 ymin,ymax (A): 0.9910001 41.33600 zmin,zma (A): -1.194000 58.72100 x,y,z range (A): 46.47700 40.34500 59.91500 scale (grids/A): 0.5941751 object centre (A): -11.93850 21.16350 28.76350 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 90.12886 89.53003 89.43966 assigned negative charge : -287.4003 centred at (gu) : 90.01142 89.69707 89.43893 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4737 nv = 96 ne = 84 npr = 40133 no. pairs analyzed = 40133 no. exposed pairs = 2434 no. arc points = 17041 no. surface atoms = 837 nbur = 1133 mkacc time = 7.0000008E-02 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 = 1.484000 m= 199 mr = 2581 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1777 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 5801 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.6149870E-10 6.2344091E-10 midg,1,midg; midg,igrid,midg 4.8843449E-09 -2.8185505E-09 1,midg,midg; igrid,midg,midg -1.9331594E-09 3.3984615E-09 gauss-seidel spectral radius is 0.9852908 estimated iterations to convergence 68 setup time was (sec) 0.3300000 now iterating at: 14:20:40 rms-change max change #iterations 8.7368511E-02 14.79298 at 10iterations 7.1508498E-03 1.174759 at 20iterations 6.0412189E-04 0.1007538 at 30iterations 4.8102607E-05 7.6103210E-03 at 40iterations 3.9935076E-06 8.0490112E-04 at 50iterations finished qdiffx linear iterations at : 14:20:43 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 3.9935076E-06 8.0490112E-04 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 14:20:43 3.412u 0.189s 0:03.89 92.2% 0+0k 0+0io 6pf+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 Wed Dec 21 2011 at 14:20:43 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.782525 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): -35.17700 11.30000 ymin,ymax (A): 0.9910001 41.33600 zmin,zma (A): -1.194000 58.72100 x,y,z range (A): 46.47700 40.34500 59.91500 scale (grids/A): 1.782525 object centre (A): -11.93850 21.16350 28.76350 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 90.38657 88.59021 88.31866 assigned negative charge : -287.4003 centred at (gu) : 90.03427 89.09146 88.31709 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 51358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17041 grid for indexing accessible points = 1.400000 m= 17881 mr = 35293 m= 2252 mr = 13310 m= 98 mr = 1316 m= 0 mr = 8 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 21662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 14342 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) : 0.5941751 object centre at (A) : -11.93850 21.16350 28.76350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3202587E-02 2.6252300E-02 midg,1,midg; midg,igrid,midg 2.1396303E-03 -1.0245446E-02 1,midg,midg; igrid,midg,midg -4.6868287E-03 5.7315425E-04 gauss-seidel spectral radius is 0.9983675 estimated iterations to convergence 196 setup time was (sec) 0.6200000 now iterating at: 14:20:44 rms-change max change #iterations 3.147337 145.7173 at 10iterations 1.373937 53.37608 at 20iterations 0.6016696 26.48290 at 30iterations 0.2616555 11.28069 at 40iterations 0.1135300 4.355473 at 50iterations 4.9703155E-02 2.111969 at 60iterations 2.1662526E-02 0.8495102 at 70iterations 9.4648423E-03 0.3785295 at 80iterations 4.1271248E-03 0.1743107 at 90iterations 1.7958363E-03 6.8126678E-02 at 100iterations 7.8330515E-04 3.3183098E-02 at 110iterations 3.4330183E-04 1.3015747E-02 at 120iterations finished qdiffx linear iterations at : 14:20:52 total time elapsed so far: 8.990000 # loops : 120 mean,max change (kT/e) : 3.4330183E-04 1.3015747E-02 energy calculations done at 8.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.110000 DelPhi exited at 14:20:53 9.111u 0.444s 0:10.02 95.3% 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 Wed Dec 21 2011 at 14:20:53 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.673788 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): -35.17700 11.30000 ymin,ymax (A): 0.9910001 41.33600 zmin,zma (A): -1.194000 58.72100 x,y,z range (A): 46.47700 40.34500 59.91500 scale (grids/A): 2.673788 object centre (A): -11.93850 21.16350 28.76350 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 90.57966 87.88520 87.47792 assigned negative charge : -287.4003 centred at (gu) : 90.05145 88.63715 87.47573 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 118689 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17041 grid for indexing accessible points = 1.400000 m= 58878 mr = 85352 m= 19863 mr = 48387 m= 3891 mr = 16194 m= 390 mr = 2721 m= 6 mr = 221 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7800000 number of dielectric boundary points 48842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 14701 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) : 1.782525 object centre at (A) : -11.93850 21.16350 28.76350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2330241E-02 0.2731322 midg,1,midg; midg,igrid,midg -1.6716536E-02 -0.1397560 1,midg,midg; igrid,midg,midg -7.9756461E-02 -3.3231847E-02 gauss-seidel spectral radius is 0.9991611 estimated iterations to convergence 273 setup time was (sec) 1.200000 now iterating at: 14:20:55 rms-change max change #iterations 7.633413 347.0098 at 10iterations 4.277641 139.2442 at 20iterations 2.385432 95.81873 at 30iterations 1.326566 60.39738 at 40iterations 0.7340530 17.56994 at 50iterations 0.4066529 8.888977 at 60iterations 0.2245991 4.874962 at 70iterations 0.1242706 2.622867 at 80iterations 6.8566576E-02 1.498302 at 90iterations 3.7924729E-02 0.8344727 at 100iterations 2.1042639E-02 0.4579401 at 110iterations 1.1645746E-02 0.2564831 at 120iterations 6.4279451E-03 0.1417990 at 130iterations 3.5526601E-03 7.6660156E-02 at 140iterations 1.9640704E-03 4.5017242E-02 at 150iterations 1.0813696E-03 2.3250103E-02 at 160iterations 5.9934298E-04 1.3678551E-02 at 170iterations 3.3166294E-04 8.9044571E-03 at 180iterations finished qdiffx linear iterations at : 14:21:10 total time elapsed so far: 16.55000 # loops : 180 mean,max change (kT/e) : 3.3166294E-04 8.9044571E-03 energy calculations done at 16.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.69000 DelPhi exited at 14:21:11 16.688u 0.465s 0:17.52 97.8% 0+0k 0+0io 0pf+0w