Sun Oct 9 11:30:08 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 11:30:08 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2925 !!! WARNING: HIR 220 has a net charge of 0.5140 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: 0.5874684 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): -18.22300 42.37600 ymin,ymax (A): -26.49500 22.68600 zmin,zma (A): -28.68800 27.04600 x,y,z range (A): 60.59900 49.18100 55.73400 scale (grids/A): 0.5874684 object centre (A): 12.07650 -1.904501 -0.8210001 number of atom coordinates read : 2925 total number of charged atoms : 2845 net assigned charge : 2.970020 assigned positive charge : 437.1509 centred at (gu) : 88.44608 90.60088 91.84540 assigned negative charge : -434.1828 centred at (gu) : 88.44933 90.57653 91.76105 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6859 nv = 96 ne = 84 npr = 56765 no. pairs analyzed = 56765 no. exposed pairs = 4070 no. arc points = 28447 no. surface atoms = 1357 nbur = 1568 mkacc time = 0.1900000 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= 333 mr = 3425 m= 3 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2825 ## 267 charges are in solution ## iepsmp to db, and charging done at 3.120000 number of grid points assigned charge 8695 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.9195840E-10 4.7178652E-09 midg,1,midg; midg,igrid,midg 1.0410971E-10 1.6553334E-09 1,midg,midg; igrid,midg,midg 1.2345738E-09 4.9158755E-10 gauss-seidel spectral radius is 0.9850499 estimated iterations to convergence 67 setup time was (sec) 3.340000 now iterating at: 11:30:12 rms-change max change #iterations 0.1030464 18.33322 at 10iterations 8.4148524E-03 1.299065 at 20iterations 8.1138057E-04 0.1267319 at 30iterations 1.3591560E-04 2.3745537E-02 at 40iterations 3.2202701E-05 5.8078766E-03 at 50iterations finished qdiffx linear iterations at : 11:30:15 total time elapsed so far: 7.060000 # loops : 50 mean,max change (kT/e) : 3.2202701E-05 5.8078766E-03 energy calculations done at 7.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 11:30:16 7.296u 0.381s 0:07.96 96.3% 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 11:30:16 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2925 !!! WARNING: HIR 220 has a net charge of 0.5140 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: 1.762405 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): -18.22300 42.37600 ymin,ymax (A): -26.49500 22.68600 zmin,zma (A): -28.68800 27.04600 x,y,z range (A): 60.59900 49.18100 55.73400 scale (grids/A): 1.762405 object centre (A): 12.07650 -1.904501 -0.8210001 number of atom coordinates read : 2925 total number of charged atoms : 2845 net assigned charge : 2.970020 assigned positive charge : 437.1509 centred at (gu) : 85.33735 91.80190 95.53515 assigned negative charge : -434.1828 centred at (gu) : 85.34785 91.72942 95.28300 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 75025 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28447 grid for indexing accessible points = 1.400000 m= 25048 mr = 49568 m= 3708 mr = 17203 m= 158 mr = 2178 m= 0 mr = 26 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 246 time to turn everything in is 0.7700000 number of dielectric boundary points 34964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 229 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 22160 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) : 0.5874684 object centre at (A) : 12.07650 -1.904501 -0.8210001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1960414E-02 1.2396863E-02 midg,1,midg; midg,igrid,midg 1.1154532E-02 2.1439446E-02 1,midg,midg; igrid,midg,midg 3.1014211E-03 -3.9581168E-03 gauss-seidel spectral radius is 0.9984644 estimated iterations to convergence 202 setup time was (sec) 1.110000 now iterating at: 11:30:18 rms-change max change #iterations 3.840516 160.2202 at 10iterations 1.711014 57.82198 at 20iterations 0.7622254 24.83756 at 30iterations 0.3405952 11.39160 at 40iterations 0.1517651 6.406785 at 50iterations 6.7962147E-02 2.333414 at 60iterations 3.0368572E-02 0.9753323 at 70iterations 1.3569936E-02 0.4529800 at 80iterations 6.0911300E-03 0.2102852 at 90iterations 2.7494130E-03 8.7512016E-02 at 100iterations 1.2411742E-03 4.6203613E-02 at 110iterations 5.6792935E-04 1.9096375E-02 at 120iterations finished qdiffx linear iterations at : 11:30:27 total time elapsed so far: 10.78000 # loops : 120 mean,max change (kT/e) : 5.6792935E-04 1.9096375E-02 energy calculations done at 10.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.00000 DelPhi exited at 11:30:28 11.009u 0.440s 0:11.73 97.5% 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 11:30:28 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2925 !!! WARNING: HIR 220 has a net charge of 0.5140 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: 2.643608 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): -18.22300 42.37600 ymin,ymax (A): -26.49500 22.68600 zmin,zma (A): -28.68800 27.04600 x,y,z range (A): 60.59900 49.18100 55.73400 scale (grids/A): 2.643608 object centre (A): 12.07650 -1.904501 -0.8210001 number of atom coordinates read : 2925 total number of charged atoms : 2845 net assigned charge : 2.970020 assigned positive charge : 437.1509 centred at (gu) : 83.00596 92.70259 98.30252 assigned negative charge : -434.1828 centred at (gu) : 83.02170 92.59404 97.92448 start vw surface at 0.1700000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 173499 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28447 grid for indexing accessible points = 1.400000 m= 82018 mr = 121526 m= 28026 mr = 63984 m= 6515 mr = 21413 m= 835 mr = 4736 m= 18 mr = 490 m= 0 mr = 2 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 881 time to turn everything in is 1.950000 number of dielectric boundary points 78760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 22744 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) : 1.762405 object centre at (A) : 12.07650 -1.904501 -0.8210001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1287010 0.1486429 midg,1,midg; midg,igrid,midg 0.1802902 0.2986365 1,midg,midg; igrid,midg,midg 4.0723763E-02 2.7405219E-02 gauss-seidel spectral radius is 0.9992275 estimated iterations to convergence 284 setup time was (sec) 2.310000 now iterating at: 11:30:31 rms-change max change #iterations 9.683764 276.0833 at 10iterations 5.672244 145.2535 at 20iterations 3.309108 78.72097 at 30iterations 1.909521 42.20798 at 40iterations 1.102058 22.87263 at 50iterations 0.6335415 14.32770 at 60iterations 0.3621626 8.393951 at 70iterations 0.2070589 4.055456 at 80iterations 0.1181667 2.184406 at 90iterations 6.7497097E-02 1.222817 at 100iterations 3.8365174E-02 0.8272171 at 110iterations 2.1881482E-02 0.4586143 at 120iterations 1.2449646E-02 0.2189369 at 130iterations 7.0797624E-03 0.1300201 at 140iterations 4.0245843E-03 8.3083630E-02 at 150iterations 2.2892847E-03 4.4036865E-02 at 160iterations 1.3020604E-03 2.3075104E-02 at 170iterations 7.4252422E-04 1.3305664E-02 at 180iterations finished qdiffx linear iterations at : 11:30:47 total time elapsed so far: 18.42000 # loops : 180 mean,max change (kT/e) : 7.4252422E-04 1.3305664E-02 energy calculations done at 18.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.66000 DelPhi exited at 11:30:47 18.660u 0.477s 0:19.50 98.1% 0+0k 0+0io 0pf+0w