Sat Oct 15 15:14:25 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 Sat Oct 15 2011 at 15:14:25 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2875 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: SEP 233 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6581867 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): 55.98000 108.1070 ymin,ymax (A): 6.345000 58.96800 zmin,zma (A): 4.958000 59.04600 x,y,z range (A): 52.12700 52.62300 54.08800 scale (grids/A): 0.6581867 object centre (A): 82.04350 32.65650 32.00200 number of atom coordinates read : 2875 total number of charged atoms : 2719 net assigned charge : 0.7010221 assigned positive charge : 437.5097 centred at (gu) : 90.97856 90.15240 90.91855 assigned negative charge : -436.8091 centred at (gu) : 90.79878 90.34308 90.82458 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8371 nv = 96 ne = 84 npr = 58792 no. pairs analyzed = 58792 no. exposed pairs = 3431 no. arc points = 24542 no. surface atoms = 1149 nbur = 1726 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 491 mr = 4778 m= 5 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 91 time to turn everything in is 0.2100000 number of dielectric boundary points 4023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2332 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9830 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5562028E-08 2.5519777E-08 midg,1,midg; midg,igrid,midg 3.9605492E-08 -4.1420581E-08 1,midg,midg; igrid,midg,midg -3.0612178E-08 4.7670760E-08 gauss-seidel spectral radius is 0.9880606 estimated iterations to convergence 75 setup time was (sec) 0.4200000 now iterating at: 15:14:26 rms-change max change #iterations 0.1807446 28.35209 at 10iterations 1.9072285E-02 2.778796 at 20iterations 2.0391252E-03 0.2650681 at 30iterations 2.1974501E-04 2.9650688E-02 at 40iterations 2.6566691E-05 3.7841797E-03 at 50iterations finished qdiffx linear iterations at : 15:14:32 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 2.6566691E-05 3.7841797E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 15:14:32 3.557u 0.206s 0:06.80 55.1% 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 Sat Oct 15 2011 at 15:14:32 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2875 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: SEP 233 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.974560 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): 55.98000 108.1070 ymin,ymax (A): 6.345000 58.96800 zmin,zma (A): 4.958000 59.04600 x,y,z range (A): 52.12700 52.62300 54.08800 scale (grids/A): 1.974560 object centre (A): 82.04350 32.65650 32.00200 number of atom coordinates read : 2875 total number of charged atoms : 2719 net assigned charge : 0.7010221 assigned positive charge : 437.5097 centred at (gu) : 92.93527 90.45667 92.75496 assigned negative charge : -436.8091 centred at (gu) : 92.39577 91.02875 92.47339 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 89137 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24542 grid for indexing accessible points = 1.400000 m= 35184 mr = 62603 m= 6219 mr = 26910 m= 383 mr = 4157 m= 9 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 850 time to turn everything in is 0.4400000 number of dielectric boundary points 37097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 21470 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) : 0.6581867 object centre at (A) : 82.04350 32.65650 32.00200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0890497E-02 -3.3602089E-02 midg,1,midg; midg,igrid,midg 6.2167585E-02 -7.9901583E-02 1,midg,midg; igrid,midg,midg -1.2507848E-02 9.7010382E-02 gauss-seidel spectral radius is 0.9987555 estimated iterations to convergence 224 setup time was (sec) 0.6700000 now iterating at: 15:14:33 rms-change max change #iterations 4.923450 222.8706 at 10iterations 2.392946 75.96896 at 20iterations 1.157773 34.69468 at 30iterations 0.5638028 16.16206 at 40iterations 0.2739518 7.883972 at 50iterations 0.1328380 4.076660 at 60iterations 6.4492740E-02 1.905031 at 70iterations 3.1279910E-02 0.8723297 at 80iterations 1.5208542E-02 0.4712462 at 90iterations 7.3957304E-03 0.2212067 at 100iterations 3.6110573E-03 0.1111240 at 110iterations 1.7620915E-03 5.0149918E-02 at 120iterations finished qdiffx linear iterations at : 15:14:48 total time elapsed so far: 8.180000 # loops : 120 mean,max change (kT/e) : 1.7620915E-03 5.0149918E-02 energy calculations done at 8.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.310000 DelPhi exited at 15:14:49 8.313u 0.244s 0:16.48 51.8% 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 Sat Oct 15 2011 at 15:14:49 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2875 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: SEP 233 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.961840 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): 55.98000 108.1070 ymin,ymax (A): 6.345000 58.96800 zmin,zma (A): 4.958000 59.04600 x,y,z range (A): 52.12700 52.62300 54.08800 scale (grids/A): 2.961840 object centre (A): 82.04350 32.65650 32.00200 number of atom coordinates read : 2875 total number of charged atoms : 2719 net assigned charge : 0.7010221 assigned positive charge : 437.5097 centred at (gu) : 94.40271 90.68491 94.13243 assigned negative charge : -436.8091 centred at (gu) : 93.59357 91.54299 93.70988 start vw surface at 0.1000000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 205455 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24542 grid for indexing accessible points = 1.400000 m= 110312 mr = 150664 m= 43972 mr = 92107 m= 11572 mr = 36523 m= 1755 mr = 9025 m= 136 mr = 1283 m= 4 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 2856 time to turn everything in is 1.190000 number of dielectric boundary points 83551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 21750 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) : 1.974560 object centre at (A) : 82.04350 32.65650 32.00200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9717455E-02 -1.043612 midg,1,midg; midg,igrid,midg 0.6392286 -1.185576 1,midg,midg; igrid,midg,midg 0.1728479 0.9303272 gauss-seidel spectral radius is 0.9992924 estimated iterations to convergence 297 setup time was (sec) 1.450000 now iterating at: 15:14:51 rms-change max change #iterations 11.19900 393.1575 at 10iterations 6.582109 141.9405 at 20iterations 3.865585 72.71680 at 30iterations 2.267673 38.72884 at 40iterations 1.326508 21.02786 at 50iterations 0.7760482 12.66621 at 60iterations 0.4541372 8.236576 at 70iterations 0.2652955 4.799225 at 80iterations 0.1548605 2.528854 at 90iterations 9.0224601E-02 1.512878 at 100iterations 5.2561522E-02 0.9052892 at 110iterations 3.0594675E-02 0.5087287 at 120iterations 1.7843315E-02 0.3161926 at 130iterations 1.0416101E-02 0.1737061 at 140iterations 6.0691107E-03 0.1031342 at 150iterations 3.5391592E-03 5.5238724E-02 at 160iterations 2.0596944E-03 3.2508850E-02 at 170iterations 1.2025817E-03 2.0130157E-02 at 180iterations finished qdiffx linear iterations at : 15:15:15 total time elapsed so far: 13.67000 # loops : 180 mean,max change (kT/e) : 1.2025817E-03 2.0130157E-02 energy calculations done at 13.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.80000 DelPhi exited at 15:15:16 13.802u 0.244s 0:27.17 51.6% 0+0k 0+0io 0pf+0w