Tue Oct 11 08:22:21 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 Tue Oct 11 2011 at 08:22:21 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2800 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6598458 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): -9.562000 36.86600 ymin,ymax (A): -27.49000 21.70900 zmin,zma (A): -8.268000 45.68400 x,y,z range (A): 46.42800 49.19900 53.95200 scale (grids/A): 0.6598458 object centre (A): 13.65200 -2.890500 18.70800 number of atom coordinates read : 2800 total number of charged atoms : 2648 net assigned charge : 4.162019 assigned positive charge : 421.9037 centred at (gu) : 89.42207 90.56678 91.03069 assigned negative charge : -417.7422 centred at (gu) : 89.11590 90.42620 91.03455 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8187 nv = 96 ne = 84 npr = 57144 no. pairs analyzed = 57144 no. exposed pairs = 3332 no. arc points = 22979 no. surface atoms = 1127 nbur = 1673 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 448 mr = 4756 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3400000 number of dielectric boundary points 3817 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2263 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9687 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5250705E-09 1.2401866E-08 midg,1,midg; midg,igrid,midg -1.7072722E-08 4.5308933E-08 1,midg,midg; igrid,midg,midg -6.3556570E-08 6.5263684E-08 gauss-seidel spectral radius is 0.9881102 estimated iterations to convergence 75 setup time was (sec) 0.5900000 now iterating at: 08:22:22 rms-change max change #iterations 0.1740917 22.69025 at 10iterations 1.8748235E-02 2.290374 at 20iterations 2.0735958E-03 0.2554398 at 30iterations 2.7045610E-04 3.7513733E-02 at 40iterations 5.0163722E-05 6.6604614E-03 at 50iterations finished qdiffx linear iterations at : 08:22:24 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 5.0163722E-05 6.6604614E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 08:22:25 3.349u 0.134s 0:04.03 86.1% 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 Tue Oct 11 2011 at 08:22:25 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2800 !!! 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.979537 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): -9.562000 36.86600 ymin,ymax (A): -27.49000 21.70900 zmin,zma (A): -8.268000 45.68400 x,y,z range (A): 46.42800 49.19900 53.95200 scale (grids/A): 1.979537 object centre (A): 13.65200 -2.890500 18.70800 number of atom coordinates read : 2800 total number of charged atoms : 2648 net assigned charge : 4.162019 assigned positive charge : 421.9037 centred at (gu) : 88.26570 91.69987 93.09150 assigned negative charge : -417.7422 centred at (gu) : 87.34748 91.27815 93.10338 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 88278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22979 grid for indexing accessible points = 1.400000 m= 33940 mr = 63337 m= 5548 mr = 25908 m= 385 mr = 3611 m= 9 mr = 182 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 936 time to turn everything in is 0.6900000 number of dielectric boundary points 35122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20919 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) : 0.6598458 object centre at (A) : 13.65200 -2.890500 18.70800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9271195E-03 6.2501347E-03 midg,1,midg; midg,igrid,midg -1.2108288E-02 3.4599021E-02 1,midg,midg; igrid,midg,midg -2.4433309E-02 7.0195243E-02 gauss-seidel spectral radius is 0.9987485 estimated iterations to convergence 224 setup time was (sec) 0.9700000 now iterating at: 08:22:26 rms-change max change #iterations 4.790381 269.5191 at 10iterations 2.325706 70.03998 at 20iterations 1.124373 32.25381 at 30iterations 0.5454230 18.49409 at 40iterations 0.2648209 7.406813 at 50iterations 0.1282732 3.693284 at 60iterations 6.2261160E-02 1.745478 at 70iterations 3.0226095E-02 0.9425392 at 80iterations 1.4612992E-02 0.4096079 at 90iterations 7.1025412E-03 0.1961823 at 100iterations 3.4430879E-03 0.1128387 at 110iterations 1.6704190E-03 4.7936440E-02 at 120iterations finished qdiffx linear iterations at : 08:22:33 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 1.6704190E-03 4.7936440E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 08:22:34 7.758u 0.177s 0:08.51 93.0% 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 08:22:34 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2800 !!! 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.969306 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): -9.562000 36.86600 ymin,ymax (A): -27.49000 21.70900 zmin,zma (A): -8.268000 45.68400 x,y,z range (A): 46.42800 49.19900 53.95200 scale (grids/A): 2.969306 object centre (A): 13.65200 -2.890500 18.70800 number of atom coordinates read : 2800 total number of charged atoms : 2648 net assigned charge : 4.162019 assigned positive charge : 421.9037 centred at (gu) : 87.39822 92.54979 94.63709 assigned negative charge : -417.7422 centred at (gu) : 86.02106 91.91723 94.65498 start vw surface at 0.2400000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 203615 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22979 grid for indexing accessible points = 1.400000 m= 108616 mr = 152459 m= 41332 mr = 90733 m= 10166 mr = 34050 m= 1703 mr = 7902 m= 135 mr = 1264 m= 2 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 3309 time to turn everything in is 1.740000 number of dielectric boundary points 79086 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 21184 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) : 1.979537 object centre at (A) : 13.65200 -2.890500 18.70800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3628789E-02 0.2755192 midg,1,midg; midg,igrid,midg -0.1578508 0.3852996 1,midg,midg; igrid,midg,midg -0.1572762 0.6175817 gauss-seidel spectral radius is 0.9992854 estimated iterations to convergence 295 setup time was (sec) 2.040000 now iterating at: 08:22:36 rms-change max change #iterations 10.91392 385.7891 at 10iterations 6.433059 160.0507 at 20iterations 3.776132 70.60286 at 30iterations 2.215249 39.81505 at 40iterations 1.293170 23.98009 at 50iterations 0.7572718 14.13234 at 60iterations 0.4419589 8.539179 at 70iterations 0.2584065 5.042459 at 80iterations 0.1505542 2.448429 at 90iterations 8.7744243E-02 1.561935 at 100iterations 5.1111206E-02 0.8223305 at 110iterations 2.9763401E-02 0.4967003 at 120iterations 1.7341286E-02 0.3264389 at 130iterations 1.0135992E-02 0.1749191 at 140iterations 5.9387847E-03 9.7582817E-02 at 150iterations 3.4979319E-03 5.9473991E-02 at 160iterations 2.0751453E-03 3.8409233E-02 at 170iterations 1.2496244E-03 2.1905899E-02 at 180iterations finished qdiffx linear iterations at : 08:22:47 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 1.2496244E-03 2.1905899E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 08:22:48 13.544u 0.207s 0:14.43 95.2% 0+0k 0+0io 0pf+0w