Tue Oct 11 08:33:52 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+sph2.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 = amb2.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 08:33:52 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2079 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.6973829 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): -19.26800 23.86200 ymin,ymax (A): -12.39200 28.74400 zmin,zma (A): -2.923000 48.12500 x,y,z range (A): 43.13000 41.13600 51.04800 scale (grids/A): 0.6973829 object centre (A): 2.297000 8.176001 22.60100 number of atom coordinates read : 2079 total number of charged atoms : 1958 net assigned charge : 5.564011 assigned positive charge : 319.6460 centred at (gu) : 89.80851 89.74467 90.55905 assigned negative charge : -314.0821 centred at (gu) : 89.68535 89.76941 90.62225 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6885 nv = 96 ne = 84 npr = 41247 no. pairs analyzed = 41247 no. exposed pairs = 2529 no. arc points = 17241 no. surface atoms = 860 nbur = 1219 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 443 mr = 3969 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1650 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7699 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5661715E-08 1.3108574E-08 midg,1,midg; midg,igrid,midg 4.9322896E-08 2.6061290E-08 1,midg,midg; igrid,midg,midg -1.2853691E-08 8.2228766E-08 gauss-seidel spectral radius is 0.9892844 estimated iterations to convergence 79 setup time was (sec) 0.5600000 now iterating at: 08:33:53 rms-change max change #iterations 0.1921709 27.50051 at 10iterations 2.3281837E-02 3.429977 at 20iterations 3.2847417E-03 0.4606438 at 30iterations 6.2520429E-04 7.7465057E-02 at 40iterations 1.7004882E-04 2.1558762E-02 at 50iterations finished qdiffx linear iterations at : 08:33:57 total time elapsed so far: 4.510000 # loops : 50 mean,max change (kT/e) : 1.7004882E-04 2.1558762E-02 energy calculations done at 4.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.660000 DelPhi exited at 08:33:58 4.668u 0.397s 0:05.56 90.8% 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 Tue Oct 11 2011 at 08:33:58 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2079 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.092149 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): -19.26800 23.86200 ymin,ymax (A): -12.39200 28.74400 zmin,zma (A): -2.923000 48.12500 x,y,z range (A): 43.13000 41.13600 51.04800 scale (grids/A): 2.092149 object centre (A): 2.297000 8.176001 22.60100 number of atom coordinates read : 2079 total number of charged atoms : 1958 net assigned charge : 5.564011 assigned positive charge : 319.6460 centred at (gu) : 89.42532 89.23396 91.67724 assigned negative charge : -314.0821 centred at (gu) : 89.05611 89.30833 91.86682 start vw surface at 0.1000000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 73363 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17241 grid for indexing accessible points = 1.400000 m= 29816 mr = 52356 m= 5581 mr = 22751 m= 460 mr = 3662 m= 3 mr = 207 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 30247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 15539 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) : 0.6973829 object centre at (A) : 2.297000 8.176001 22.60100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8782493E-02 5.0195757E-02 midg,1,midg; midg,igrid,midg 2.2971179E-02 5.3672730E-03 1,midg,midg; igrid,midg,midg 5.3521944E-03 3.1485453E-02 gauss-seidel spectral radius is 0.9988008 estimated iterations to convergence 229 setup time was (sec) 0.9500000 now iterating at: 08:33:59 rms-change max change #iterations 4.582503 220.6078 at 10iterations 2.238095 72.86949 at 20iterations 1.103074 38.71088 at 30iterations 0.5452514 17.88006 at 40iterations 0.2677478 8.765192 at 50iterations 0.1321846 4.585494 at 60iterations 6.5251298E-02 2.258132 at 70iterations 3.2317489E-02 0.9340782 at 80iterations 1.6062187E-02 0.5218635 at 90iterations 8.0918139E-03 0.2529907 at 100iterations 4.1023819E-03 0.1352844 at 110iterations 2.1578867E-03 6.6520691E-02 at 120iterations finished qdiffx linear iterations at : 08:34:09 total time elapsed so far: 10.53000 # loops : 120 mean,max change (kT/e) : 2.1578867E-03 6.6520691E-02 energy calculations done at 10.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.69000 DelPhi exited at 08:34:09 10.693u 0.435s 0:11.41 97.4% 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 Oct 11 2011 at 08:34:09 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2079 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 3.138223 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): -19.26800 23.86200 ymin,ymax (A): -12.39200 28.74400 zmin,zma (A): -2.923000 48.12500 x,y,z range (A): 43.13000 41.13600 51.04800 scale (grids/A): 3.138223 object centre (A): 2.297000 8.176001 22.60100 number of atom coordinates read : 2079 total number of charged atoms : 1958 net assigned charge : 5.564011 assigned positive charge : 319.6460 centred at (gu) : 89.13802 88.85099 92.51570 assigned negative charge : -314.0821 centred at (gu) : 88.58419 88.96249 92.80017 start vw surface at 0.1100000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 169263 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17241 grid for indexing accessible points = 1.400000 m= 92592 mr = 126254 m= 37620 mr = 77136 m= 10464 mr = 30991 m= 1982 mr = 8039 m= 192 mr = 1442 m= 3 mr = 110 m= 0 mr = 2 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.880000 number of dielectric boundary points 68142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 15656 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) : 2.092149 object centre at (A) : 2.297000 8.176001 22.60100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1790850 0.6178017 midg,1,midg; midg,igrid,midg 0.1715006 2.1742567E-02 1,midg,midg; igrid,midg,midg 0.1915927 0.2847855 gauss-seidel spectral radius is 0.9992859 estimated iterations to convergence 295 setup time was (sec) 2.220000 now iterating at: 08:34:12 rms-change max change #iterations 10.19996 366.8296 at 10iterations 6.038040 124.9920 at 20iterations 3.554721 75.71193 at 30iterations 2.088166 42.40871 at 40iterations 1.227392 22.77819 at 50iterations 0.7178598 12.92905 at 60iterations 0.4210411 9.298557 at 70iterations 0.2457770 5.072588 at 80iterations 0.1435074 2.481660 at 90iterations 8.4166564E-02 1.601849 at 100iterations 4.9250241E-02 0.8272684 at 110iterations 2.9012553E-02 0.5294876 at 120iterations 1.7193221E-02 0.3157463 at 130iterations 1.0360004E-02 0.1942139 at 140iterations 6.4298697E-03 0.1235523 at 150iterations 4.1496558E-03 8.0947876E-02 at 160iterations 2.8302222E-03 5.2787781E-02 at 170iterations 2.0451099E-03 3.6968231E-02 at 180iterations finished qdiffx linear iterations at : 08:34:29 total time elapsed so far: 18.95000 # loops : 180 mean,max change (kT/e) : 2.0451099E-03 3.6968231E-02 energy calculations done at 18.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.11000 DelPhi exited at 08:34:29 19.111u 0.468s 0:20.06 97.5% 0+0k 0+0io 0pf+0w