Tue Nov 22 14:10:52 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 Tue Nov 22 2011 at 14:10:56 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 = 1958 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: 0.6085470 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): -34.78800 10.15900 ymin,ymax (A): 0.4570001 41.67900 zmin,zma (A): -1.696000 56.80400 x,y,z range (A): 44.94700 41.22200 58.50000 scale (grids/A): 0.6085470 object centre (A): -12.31450 21.06800 27.55400 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 3.000004 assigned positive charge : 287.5540 centred at (gu) : 90.22268 89.63897 90.23021 assigned negative charge : -284.5543 centred at (gu) : 90.16237 89.78491 90.23711 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4948 nv = 96 ne = 84 npr = 40192 no. pairs analyzed = 40192 no. exposed pairs = 2528 no. arc points = 17536 no. surface atoms = 858 nbur = 1100 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 233 mr = 2659 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2500000 number of dielectric boundary points 2497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1783 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 5929 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8175267E-09 1.5039040E-09 midg,1,midg; midg,igrid,midg 7.2266486E-09 -3.2048701E-09 1,midg,midg; igrid,midg,midg -4.1357009E-10 3.9448333E-09 gauss-seidel spectral radius is 0.9859664 estimated iterations to convergence 69 setup time was (sec) 0.5200000 now iterating at: 14:11:00 rms-change max change #iterations 9.7167172E-02 17.97160 at 10iterations 8.5127866E-03 1.632729 at 20iterations 7.2451250E-04 0.1316404 at 30iterations 6.5033462E-05 1.0994911E-02 at 40iterations 5.5948904E-06 8.7738037E-04 at 50iterations finished qdiffx linear iterations at : 14:11:09 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 5.5948904E-06 8.7738037E-04 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 14:11:13 3.615u 0.207s 0:17.37 21.9% 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 Nov 22 2011 at 14:11:17 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 = 1958 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: 1.825641 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): -34.78800 10.15900 ymin,ymax (A): 0.4570001 41.67900 zmin,zma (A): -1.696000 56.80400 x,y,z range (A): 44.94700 41.22200 58.50000 scale (grids/A): 1.825641 object centre (A): -12.31450 21.06800 27.55400 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 3.000004 assigned positive charge : 287.5540 centred at (gu) : 90.66821 88.91650 90.69063 assigned negative charge : -284.5543 centred at (gu) : 90.48711 89.35493 90.71134 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 52894 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17536 grid for indexing accessible points = 1.400000 m= 19170 mr = 35993 m= 2870 mr = 14122 m= 152 mr = 1782 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 23128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 14287 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) : 0.6085470 object centre at (A) : -12.31450 21.06800 27.55400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6554162E-02 2.8811639E-02 midg,1,midg; midg,igrid,midg 5.1043951E-03 -6.9485130E-03 1,midg,midg; igrid,midg,midg -4.7164946E-03 -1.9307048E-03 gauss-seidel spectral radius is 0.9984401 estimated iterations to convergence 201 setup time was (sec) 0.6900000 now iterating at: 14:11:22 rms-change max change #iterations 3.282174 173.6761 at 10iterations 1.456547 62.23749 at 20iterations 0.6468310 25.07827 at 30iterations 0.2873253 10.58724 at 40iterations 0.1279231 4.509591 at 50iterations 5.6474019E-02 2.153955 at 60iterations 2.5214856E-02 0.9900168 at 70iterations 1.1141029E-02 0.4426208 at 80iterations 4.9190577E-03 0.1740732 at 90iterations 2.2022480E-03 8.4281921E-02 at 100iterations 9.7573525E-04 3.8121223E-02 at 110iterations 4.3469775E-04 1.6433716E-02 at 120iterations finished qdiffx linear iterations at : 14:11:43 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 4.3469775E-04 1.6433716E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 14:11:44 7.588u 0.208s 0:27.36 28.4% 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 Nov 22 2011 at 14:11:46 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 = 1958 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: 2.738461 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): -34.78800 10.15900 ymin,ymax (A): 0.4570001 41.67900 zmin,zma (A): -1.696000 56.80400 x,y,z range (A): 44.94700 41.22200 58.50000 scale (grids/A): 2.738461 object centre (A): -12.31450 21.06800 27.55400 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 3.000004 assigned positive charge : 287.5540 centred at (gu) : 91.00228 88.37500 91.03587 assigned negative charge : -284.5543 centred at (gu) : 90.73081 89.03253 91.06707 start vw surface at 0.1200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 122139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17536 grid for indexing accessible points = 1.400000 m= 62106 mr = 87154 m= 22290 mr = 50787 m= 5067 mr = 17957 m= 639 mr = 3769 m= 32 mr = 428 m= 0 mr = 6 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.020000 number of dielectric boundary points 52172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 14605 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) : 1.825641 object centre at (A) : -12.31450 21.06800 27.55400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1638820E-02 0.3227572 midg,1,midg; midg,igrid,midg -2.5768725E-03 -9.8060459E-02 1,midg,midg; igrid,midg,midg -8.3449550E-02 -6.4092472E-02 gauss-seidel spectral radius is 0.9991853 estimated iterations to convergence 277 setup time was (sec) 1.330000 now iterating at: 14:11:53 rms-change max change #iterations 7.999927 299.2033 at 10iterations 4.564634 111.6229 at 20iterations 2.595124 63.34182 at 30iterations 1.461300 39.10995 at 40iterations 0.8223798 20.62696 at 50iterations 0.4614655 10.12415 at 60iterations 0.2586357 5.536359 at 70iterations 0.1443334 2.965256 at 80iterations 8.0803126E-02 1.652847 at 90iterations 4.5126379E-02 1.061182 at 100iterations 2.5264766E-02 0.5576887 at 110iterations 1.4080299E-02 0.3097105 at 120iterations 7.8497706E-03 0.1578054 at 130iterations 4.3909550E-03 9.4017029E-02 at 140iterations 2.4452400E-03 5.1246643E-02 at 150iterations 1.3687933E-03 3.1383514E-02 at 160iterations 7.6304871E-04 1.5804768E-02 at 170iterations 4.2570723E-04 8.8653564E-03 at 180iterations finished qdiffx linear iterations at : 14:12:24 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 4.2570723E-04 8.8653564E-03 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.82000 DelPhi exited at 14:12:27 11.819u 0.216s 0:40.78 29.4% 0+0k 0+0io 0pf+0w