Tue Oct 11 06:59:24 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 06:59:24 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3012 !!! WARNING: UMP 317 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5915193 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): -15.59900 44.58500 ymin,ymax (A): 19.40700 77.13000 zmin,zma (A): -70.29700 -21.57600 x,y,z range (A): 60.18400 57.72300 48.72100 scale (grids/A): 0.5915193 object centre (A): 14.49300 48.26850 -45.93650 number of atom coordinates read : 3012 total number of charged atoms : 2869 net assigned charge : -4.099988 assigned positive charge : 438.1294 centred at (gu) : 89.25549 89.74751 90.32071 assigned negative charge : -442.2299 centred at (gu) : 89.25538 89.97913 90.29144 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6902 nv = 96 ne = 84 npr = 63572 no. pairs analyzed = 63572 no. exposed pairs = 3777 no. arc points = 26160 no. surface atoms = 1282 nbur = 1730 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 344 mr = 3749 m= 0 mr = 39 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2593 ## 288 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8758 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1175783E-09 -4.3938386E-10 midg,1,midg; midg,igrid,midg 6.1996732E-09 -8.4150784E-09 1,midg,midg; igrid,midg,midg -1.5893026E-09 -1.1346403E-09 gauss-seidel spectral radius is 0.9852467 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 06:59:25 rms-change max change #iterations 0.1067452 16.67918 at 10iterations 8.9593204E-03 1.559360 at 20iterations 7.4526912E-04 0.1207237 at 30iterations 6.9966416E-05 1.1301041E-02 at 40iterations 1.0504058E-05 2.1047592E-03 at 50iterations finished qdiffx linear iterations at : 06:59:29 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 1.0504058E-05 2.1047592E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 06:59:29 4.190u 0.213s 0:05.10 86.2% 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 06:59:30 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3012 !!! WARNING: UMP 317 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.774558 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): -15.59900 44.58500 ymin,ymax (A): 19.40700 77.13000 zmin,zma (A): -70.29700 -21.57600 x,y,z range (A): 60.18400 57.72300 48.72100 scale (grids/A): 1.774558 object centre (A): 14.49300 48.26850 -45.93650 number of atom coordinates read : 3012 total number of charged atoms : 2869 net assigned charge : -4.099988 assigned positive charge : 438.1294 centred at (gu) : 87.76619 89.24195 90.96146 assigned negative charge : -442.2299 centred at (gu) : 87.76575 89.93720 90.87396 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 74695 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26160 grid for indexing accessible points = 1.400000 m= 26365 mr = 51216 m= 3969 mr = 19393 m= 167 mr = 2562 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 753 time to turn everything in is 0.6700000 number of dielectric boundary points 31977 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 22353 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) : 0.5915193 object centre at (A) : 14.49300 48.26850 -45.93650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3581651E-03 2.0580275E-02 midg,1,midg; midg,igrid,midg 4.2356299E-03 -2.6524000E-02 1,midg,midg; igrid,midg,midg -2.8651001E-02 -2.4688574E-02 gauss-seidel spectral radius is 0.9984750 estimated iterations to convergence 203 setup time was (sec) 1.000000 now iterating at: 06:59:31 rms-change max change #iterations 3.933040 204.9232 at 10iterations 1.764525 55.95843 at 20iterations 0.7933428 26.48740 at 30iterations 0.3555748 14.66433 at 40iterations 0.1597472 5.605339 at 50iterations 7.1633153E-02 2.456745 at 60iterations 3.2186698E-02 0.9504795 at 70iterations 1.4394927E-02 0.4585190 at 80iterations 6.4787185E-03 0.2126999 at 90iterations 2.9138811E-03 9.7229004E-02 at 100iterations 1.3099500E-03 3.9646149E-02 at 110iterations 5.8942405E-04 1.7009735E-02 at 120iterations finished qdiffx linear iterations at : 06:59:39 total time elapsed so far: 9.520000 # loops : 120 mean,max change (kT/e) : 5.8942405E-04 1.7009735E-02 energy calculations done at 9.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.710000 DelPhi exited at 06:59:40 9.713u 0.248s 0:10.40 95.6% 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 06:59:40 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3012 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 2.661837 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): -15.59900 44.58500 ymin,ymax (A): 19.40700 77.13000 zmin,zma (A): -70.29700 -21.57600 x,y,z range (A): 60.18400 57.72300 48.72100 scale (grids/A): 2.661837 object centre (A): 14.49300 48.26850 -45.93650 number of atom coordinates read : 3012 total number of charged atoms : 2869 net assigned charge : -4.099988 assigned positive charge : 438.1294 centred at (gu) : 86.64892 88.86275 91.44190 assigned negative charge : -442.2299 centred at (gu) : 86.64869 89.90565 91.31083 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 172854 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26160 grid for indexing accessible points = 1.400000 m= 85613 mr = 124697 m= 30605 mr = 69419 m= 7036 mr = 24718 m= 843 mr = 5403 m= 44 mr = 563 m= 0 mr = 17 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 2758 time to turn everything in is 1.490000 number of dielectric boundary points 72178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 22948 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) : 1.774558 object centre at (A) : 14.49300 48.26850 -45.93650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6114188E-02 0.3397431 midg,1,midg; midg,igrid,midg -2.4369251E-02 -0.1918309 1,midg,midg; igrid,midg,midg -0.3218667 -0.3211987 gauss-seidel spectral radius is 0.9992297 estimated iterations to convergence 284 setup time was (sec) 1.840000 now iterating at: 06:59:42 rms-change max change #iterations 9.727542 315.2992 at 10iterations 5.661565 128.6746 at 20iterations 3.272875 80.24770 at 30iterations 1.881281 38.39989 at 40iterations 1.076776 22.08688 at 50iterations 0.6171683 12.99307 at 60iterations 0.3522333 7.073756 at 70iterations 0.2011272 4.022241 at 80iterations 0.1143295 2.239008 at 90iterations 6.5240555E-02 1.169560 at 100iterations 3.7013218E-02 0.6575144 at 110iterations 2.1081885E-02 0.4850696 at 120iterations 1.1980536E-02 0.2160969 at 130iterations 6.7954645E-03 0.1302135 at 140iterations 3.8556973E-03 7.7348709E-02 at 150iterations 2.1908288E-03 3.8652658E-02 at 160iterations 1.2466374E-03 2.5390625E-02 at 170iterations 7.0732308E-04 1.3278961E-02 at 180iterations finished qdiffx linear iterations at : 06:59:56 total time elapsed so far: 15.41000 # loops : 180 mean,max change (kT/e) : 7.0732308E-04 1.3278961E-02 energy calculations done at 15.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.60000 DelPhi exited at 06:59:56 15.599u 0.275s 0:16.17 98.0% 0+0k 0+0io 0pf+0w