Sun Oct 9 22:58:49 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 Sun Oct 9 2011 at 22:58:50 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4379 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: 0.5115750 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): -20.87700 31.22000 ymin,ymax (A): -30.39800 39.19100 zmin,zma (A): -64.29900 -0.2050000 x,y,z range (A): 52.09700 69.58900 64.09399 scale (grids/A): 0.5115750 object centre (A): 5.171501 4.396502 -32.25200 number of atom coordinates read : 4379 total number of charged atoms : 4219 net assigned charge : 4.000007 assigned positive charge : 665.2228 centred at (gu) : 89.30698 89.34268 91.68037 assigned negative charge : -661.2272 centred at (gu) : 89.44769 89.27659 91.76404 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7383 nv = 96 ne = 84 npr = 85416 no. pairs analyzed = 85416 no. exposed pairs = 5981 no. arc points = 41954 no. surface atoms = 1995 nbur = 2384 mkacc time = 0.1500000 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 = 1.708000 m= 257 mr = 3582 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4114 ## 642 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 9978 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7259978E-10 -2.3649022E-10 midg,1,midg; midg,igrid,midg -1.2502641E-10 1.8935394E-10 1,midg,midg; igrid,midg,midg 4.8828291E-10 -2.4530422E-10 gauss-seidel spectral radius is 0.9804420 estimated iterations to convergence 59 setup time was (sec) 0.4900000 now iterating at: 22:58:50 rms-change max change #iterations 6.5013453E-02 10.65024 at 10iterations 3.5871544E-03 0.5242157 at 20iterations 2.9246430E-04 5.9753418E-02 at 30iterations 7.1358882E-05 1.8373489E-02 at 40iterations 2.3739060E-05 6.1926842E-03 at 50iterations finished qdiffx linear iterations at : 22:58:53 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 2.3739060E-05 6.1926842E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 22:58:53 3.531u 0.160s 0:04.01 92.0% 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 Sun Oct 9 2011 at 22:58:54 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4379 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: 1.534725 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): -20.87700 31.22000 ymin,ymax (A): -30.39800 39.19100 zmin,zma (A): -64.29900 -0.2050000 x,y,z range (A): 52.09700 69.58900 64.09399 scale (grids/A): 1.534725 object centre (A): 5.171501 4.396502 -32.25200 number of atom coordinates read : 4379 total number of charged atoms : 4219 net assigned charge : 4.000007 assigned positive charge : 665.2228 centred at (gu) : 87.91909 88.02639 95.03957 assigned negative charge : -661.2272 centred at (gu) : 88.34271 87.82931 95.29190 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83666 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41954 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 23310 mr = 55357 m= 1888 mr = 15049 m= 44 mr = 719 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 266 time to turn everything in is 0.4100000 number of dielectric boundary points 37783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 594 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 31697 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) : 0.5115750 object centre at (A) : 5.171501 4.396502 -32.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7059170E-03 8.4007736E-03 midg,1,midg; midg,igrid,midg 1.6221855E-03 2.5232973E-02 1,midg,midg; igrid,midg,midg 1.4067324E-03 -1.0220317E-02 gauss-seidel spectral radius is 0.9980981 estimated iterations to convergence 182 setup time was (sec) 0.6200000 now iterating at: 22:58:54 rms-change max change #iterations 3.605998 159.1687 at 10iterations 1.468295 62.68655 at 20iterations 0.5985783 22.63684 at 30iterations 0.2440621 8.474953 at 40iterations 9.8960124E-02 3.286232 at 50iterations 4.0638547E-02 1.453863 at 60iterations 1.6530899E-02 0.5283184 at 70iterations 6.7770472E-03 0.2258759 at 80iterations 2.7800566E-03 9.0743065E-02 at 90iterations 1.1512234E-03 3.8488388E-02 at 100iterations 4.8846588E-04 1.7437458E-02 at 110iterations 2.1861654E-04 9.6998215E-03 at 120iterations finished qdiffx linear iterations at : 22:59:02 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 2.1861654E-04 9.6998215E-03 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 22:59:02 7.900u 0.216s 0:08.49 95.5% 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 Sun Oct 9 2011 at 22:59:02 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4379 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: 2.302088 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): -20.87700 31.22000 ymin,ymax (A): -30.39800 39.19100 zmin,zma (A): -64.29900 -0.2050000 x,y,z range (A): 52.09700 69.58900 64.09399 scale (grids/A): 2.302088 object centre (A): 5.171501 4.396502 -32.25200 number of atom coordinates read : 4379 total number of charged atoms : 4219 net assigned charge : 4.000007 assigned positive charge : 665.2228 centred at (gu) : 86.87826 87.03921 97.55899 assigned negative charge : -661.2272 centred at (gu) : 87.51394 86.74375 97.93761 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 194822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41954 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 84364 mr = 136561 m= 20389 mr = 64798 m= 2721 mr = 14234 m= 144 mr = 1501 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 862 time to turn everything in is 0.9800000 number of dielectric boundary points 85305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 33654 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) : 1.534725 object centre at (A) : 5.171501 4.396502 -32.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1625285 0.2537286 midg,1,midg; midg,igrid,midg 6.8346068E-02 0.6568591 1,midg,midg; igrid,midg,midg -7.2385664E-03 -0.1518995 gauss-seidel spectral radius is 0.9991556 estimated iterations to convergence 272 setup time was (sec) 1.220000 now iterating at: 22:59:03 rms-change max change #iterations 9.962532 285.5620 at 10iterations 5.766228 152.2010 at 20iterations 3.281102 74.05489 at 30iterations 1.858166 45.47940 at 40iterations 1.044998 21.68875 at 50iterations 0.5861608 12.55021 at 60iterations 0.3281137 7.627797 at 70iterations 0.1832489 3.701561 at 80iterations 0.1020655 1.999169 at 90iterations 5.6718443E-02 1.139490 at 100iterations 3.1587593E-02 0.6214547 at 110iterations 1.7520258E-02 0.3406448 at 120iterations 9.7233113E-03 0.1878406 at 130iterations 5.3996984E-03 0.1085663 at 140iterations 2.9919383E-03 5.4508209E-02 at 150iterations 1.6587487E-03 3.1622410E-02 at 160iterations 9.2262670E-04 1.7990112E-02 at 170iterations 5.1182910E-04 9.1438293E-03 at 180iterations finished qdiffx linear iterations at : 22:59:15 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 5.1182910E-04 9.1438293E-03 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 22:59:15 12.905u 0.215s 0:13.38 97.9% 0+0k 0+0io 0pf+0w