Tue Oct 11 06:04:16 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 06:04:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 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: 0.7359478 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): -9.108000 35.03500 ymin,ymax (A): -3.635000 34.14500 zmin,zma (A): 1.179000 49.55200 x,y,z range (A): 44.14300 37.77999 48.37300 scale (grids/A): 0.7359478 object centre (A): 12.96350 15.25500 25.36550 number of atom coordinates read : 2010 total number of charged atoms : 1891 net assigned charge : 6.500006 assigned positive charge : 305.3170 centred at (gu) : 90.15980 89.52871 91.42062 assigned negative charge : -298.8172 centred at (gu) : 89.97714 89.58495 91.48782 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7635 nv = 96 ne = 84 npr = 39972 no. pairs analyzed = 39972 no. exposed pairs = 2468 no. arc points = 16756 no. surface atoms = 840 nbur = 1170 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 568 mr = 4487 m= 7 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1491 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8035 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2590870E-07 5.8755205E-08 midg,1,midg; midg,igrid,midg 1.6805934E-07 5.1705616E-08 1,midg,midg; igrid,midg,midg -5.4756232E-08 2.6961146E-07 gauss-seidel spectral radius is 0.9903646 estimated iterations to convergence 83 setup time was (sec) 0.5400000 now iterating at: 06:04:17 rms-change max change #iterations 0.2313365 31.49558 at 10iterations 3.1025941E-02 3.953726 at 20iterations 4.1779061E-03 0.6618462 at 30iterations 5.9535599E-04 9.6088409E-02 at 40iterations 1.1050691E-04 1.3845444E-02 at 50iterations finished qdiffx linear iterations at : 06:04:19 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 1.1050691E-04 1.3845444E-02 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 06:04:20 3.586u 0.153s 0:04.16 89.6% 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 06:04:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 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: 2.207843 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): -9.108000 35.03500 ymin,ymax (A): -3.635000 34.14500 zmin,zma (A): 1.179000 49.55200 x,y,z range (A): 44.14300 37.77999 48.37300 scale (grids/A): 2.207843 object centre (A): 12.96350 15.25500 25.36550 number of atom coordinates read : 2010 total number of charged atoms : 1891 net assigned charge : 6.500006 assigned positive charge : 305.3170 centred at (gu) : 90.47944 88.58611 94.26163 assigned negative charge : -298.8172 centred at (gu) : 89.93160 88.75496 94.46375 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 79960 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16756 grid for indexing accessible points = 1.400000 m= 34177 mr = 57315 m= 7353 mr = 26553 m= 805 mr = 5055 m= 23 mr = 462 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 32933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 15067 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) : 0.7359478 object centre at (A) : 12.96350 15.25500 25.36550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6256935E-02 2.0142909E-02 midg,1,midg; midg,igrid,midg 3.8387075E-02 9.2069954E-03 1,midg,midg; igrid,midg,midg 3.2001909E-02 6.3223176E-02 gauss-seidel spectral radius is 0.9989039 estimated iterations to convergence 239 setup time was (sec) 0.9100000 now iterating at: 06:04:21 rms-change max change #iterations 4.812251 227.8669 at 10iterations 2.440030 72.01283 at 20iterations 1.242071 37.42439 at 30iterations 0.6325927 19.81443 at 40iterations 0.3213453 8.865419 at 50iterations 0.1637205 4.993340 at 60iterations 8.3217159E-02 2.437521 at 70iterations 4.2257152E-02 1.141111 at 80iterations 2.1542363E-02 0.6041223 at 90iterations 1.0982583E-02 0.3080454 at 100iterations 5.6357323E-03 0.1699295 at 110iterations 2.9080708E-03 8.4241867E-02 at 120iterations finished qdiffx linear iterations at : 06:04:28 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 2.9080708E-03 8.4241867E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 06:04:29 7.873u 0.192s 0:08.51 94.7% 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 06:04:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 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: 3.311765 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): -9.108000 35.03500 ymin,ymax (A): -3.635000 34.14500 zmin,zma (A): 1.179000 49.55200 x,y,z range (A): 44.14300 37.77999 48.37300 scale (grids/A): 3.311765 object centre (A): 12.96350 15.25500 25.36550 number of atom coordinates read : 2010 total number of charged atoms : 1891 net assigned charge : 6.500006 assigned positive charge : 305.3170 centred at (gu) : 90.71915 87.87910 96.39240 assigned negative charge : -298.8172 centred at (gu) : 89.89745 88.13253 96.69557 start vw surface at 0.1600000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 183958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16756 grid for indexing accessible points = 1.400000 m= 104209 mr = 137323 m= 45515 mr = 87883 m= 14364 mr = 38083 m= 3170 mr = 11337 m= 451 mr = 2377 m= 11 mr = 322 m= 0 mr = 3 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.040000 number of dielectric boundary points 74350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 15128 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) : 2.207843 object centre at (A) : 12.96350 15.25500 25.36550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4077864 9.4294399E-02 midg,1,midg; midg,igrid,midg 0.3247552 6.7531630E-02 1,midg,midg; igrid,midg,midg 0.4832424 0.4887815 gauss-seidel spectral radius is 0.9993145 estimated iterations to convergence 301 setup time was (sec) 2.350000 now iterating at: 06:04:31 rms-change max change #iterations 10.52787 258.4915 at 10iterations 6.284711 133.6579 at 20iterations 3.751317 67.51855 at 30iterations 2.235188 42.08209 at 40iterations 1.324418 23.23930 at 50iterations 0.7824821 14.88223 at 60iterations 0.4643816 8.972115 at 70iterations 0.2735911 4.732704 at 80iterations 0.1618433 2.847614 at 90iterations 9.5287465E-02 1.602838 at 100iterations 5.6381762E-02 0.9722331 at 110iterations 3.3245452E-02 0.5828531 at 120iterations 1.9727517E-02 0.3443007 at 130iterations 1.1740631E-02 0.2058158 at 140iterations 7.0582577E-03 0.1388245 at 150iterations 4.3300046E-03 6.8191528E-02 at 160iterations 2.7358362E-03 4.3624878E-02 at 170iterations 1.8200682E-03 2.9534340E-02 at 180iterations finished qdiffx linear iterations at : 06:04:42 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 1.8200682E-03 2.9534340E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.34000 DelPhi exited at 06:04:42 13.338u 0.177s 0:13.83 97.6% 0+0k 0+0io 0pf+0w