Mon Oct 10 00:11:05 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 00:11:05 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 = 3111 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: 0.6331252 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): -34.79300 19.37200 ymin,ymax (A): -13.47500 37.70400 zmin,zma (A): -14.41500 41.81400 x,y,z range (A): 54.16500 51.17900 56.22900 scale (grids/A): 0.6331252 object centre (A): -7.710502 12.11450 13.69950 number of atom coordinates read : 3111 total number of charged atoms : 2969 net assigned charge : 2.500006 assigned positive charge : 469.0319 centred at (gu) : 91.02846 90.41693 91.42722 assigned negative charge : -466.5332 centred at (gu) : 91.00742 90.32108 91.39012 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8359 nv = 96 ne = 84 npr = 61899 no. pairs analyzed = 61899 no. exposed pairs = 4054 no. arc points = 28958 no. surface atoms = 1348 nbur = 1763 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 4439 m= 4 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3300000 number of dielectric boundary points 4335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2853 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 10177 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0475900E-09 9.6852464E-09 midg,1,midg; midg,igrid,midg -7.6317628E-09 1.5116848E-08 1,midg,midg; igrid,midg,midg 3.3949962E-10 6.5572330E-09 gauss-seidel spectral radius is 0.9871284 estimated iterations to convergence 72 setup time was (sec) 0.5700000 now iterating at: 00:11:06 rms-change max change #iterations 0.1491212 18.88238 at 10iterations 1.4477052E-02 1.909401 at 20iterations 1.4136927E-03 0.1977196 at 30iterations 1.3918156E-04 1.7591476E-02 at 40iterations 1.4597282E-05 1.8229485E-03 at 50iterations finished qdiffx linear iterations at : 00:11:09 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 1.4597282E-05 1.8229485E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 00:11:10 4.231u 0.273s 0:04.83 93.1% 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 00:11:10 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 = 3111 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: 1.899376 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): -34.79300 19.37200 ymin,ymax (A): -13.47500 37.70400 zmin,zma (A): -14.41500 41.81400 x,y,z range (A): 54.16500 51.17900 56.22900 scale (grids/A): 1.899376 object centre (A): -7.710502 12.11450 13.69950 number of atom coordinates read : 3111 total number of charged atoms : 2969 net assigned charge : 2.500006 assigned positive charge : 469.0319 centred at (gu) : 93.08474 91.24981 94.28112 assigned negative charge : -466.5332 centred at (gu) : 93.02199 90.96323 94.17020 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 90545 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28958 grid for indexing accessible points = 1.400000 m= 30765 mr = 61460 m= 4413 mr = 21870 m= 215 mr = 2572 m= 0 mr = 73 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 3109 time to turn everything in is 0.7300000 number of dielectric boundary points 39963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 23348 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) : 0.6331252 object centre at (A) : -7.710502 12.11450 13.69950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0270394E-02 5.3840596E-03 midg,1,midg; midg,igrid,midg -2.5702443E-03 1.4201225E-02 1,midg,midg; igrid,midg,midg -1.7294249E-02 6.4903358E-03 gauss-seidel spectral radius is 0.9986892 estimated iterations to convergence 219 setup time was (sec) 1.050000 now iterating at: 00:11:11 rms-change max change #iterations 4.651180 204.8217 at 10iterations 2.203533 75.53898 at 20iterations 1.042920 31.53430 at 30iterations 0.4960369 16.57566 at 40iterations 0.2359012 6.946880 at 50iterations 0.1117607 3.335206 at 60iterations 5.3297624E-02 1.561511 at 70iterations 2.5201639E-02 0.7258334 at 80iterations 1.2015707E-02 0.3647661 at 90iterations 5.6999540E-03 0.1687031 at 100iterations 2.7012334E-03 8.2283020E-02 at 110iterations 1.2837574E-03 3.6774635E-02 at 120iterations finished qdiffx linear iterations at : 00:11:20 total time elapsed so far: 9.710000 # loops : 120 mean,max change (kT/e) : 1.2837574E-03 3.6774635E-02 energy calculations done at 9.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.880000 DelPhi exited at 00:11:20 9.886u 0.303s 0:10.59 96.1% 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 00:11:20 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 = 3111 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: 2.849064 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): -34.79300 19.37200 ymin,ymax (A): -13.47500 37.70400 zmin,zma (A): -14.41500 41.81400 x,y,z range (A): 54.16500 51.17900 56.22900 scale (grids/A): 2.849064 object centre (A): -7.710502 12.11450 13.69950 number of atom coordinates read : 3111 total number of charged atoms : 2969 net assigned charge : 2.500006 assigned positive charge : 469.0319 centred at (gu) : 94.62682 91.87453 96.42152 assigned negative charge : -466.5332 centred at (gu) : 94.53265 91.44469 96.25498 start vw surface at 0.1800000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 209705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28958 grid for indexing accessible points = 1.400000 m= 101302 mr = 149461 m= 34379 mr = 81525 m= 7648 mr = 26797 m= 952 mr = 5538 m= 29 mr = 608 m= 0 mr = 14 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 10562 time to turn everything in is 1.810000 number of dielectric boundary points 90072 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 23750 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) : 1.899376 object centre at (A) : -7.710502 12.11450 13.69950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1629007 2.2771362E-02 midg,1,midg; midg,igrid,midg 4.8907191E-02 -0.1074896 1,midg,midg; igrid,midg,midg -0.2992407 -3.6120731E-02 gauss-seidel spectral radius is 0.9992985 estimated iterations to convergence 298 setup time was (sec) 2.170000 now iterating at: 00:11:23 rms-change max change #iterations 11.10123 392.0428 at 10iterations 6.683844 158.3177 at 20iterations 3.991806 114.1104 at 30iterations 2.366724 45.54790 at 40iterations 1.397367 25.28103 at 50iterations 0.8240677 13.89570 at 60iterations 0.4843709 8.311132 at 70iterations 0.2838521 5.035153 at 80iterations 0.1666077 4.055501 at 90iterations 9.7657792E-02 1.560972 at 100iterations 5.6949914E-02 1.036002 at 110iterations 3.3364106E-02 0.5783608 at 120iterations 1.9463612E-02 0.3257389 at 130iterations 1.1363725E-02 0.1876106 at 140iterations 6.6482625E-03 0.1214046 at 150iterations 3.8745212E-03 8.2569122E-02 at 160iterations 2.2626808E-03 3.6863089E-02 at 170iterations 1.3208993E-03 2.1948814E-02 at 180iterations finished qdiffx linear iterations at : 00:11:37 total time elapsed so far: 16.13000 # loops : 180 mean,max change (kT/e) : 1.3208993E-03 2.1948814E-02 energy calculations done at 16.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.32000 DelPhi exited at 00:11:37 16.321u 0.284s 0:16.87 98.3% 0+0k 0+0io 0pf+0w