Tue Oct 11 06:09:21 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+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 Tue Oct 11 2011 at 06:09:21 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2016 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7479150 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): -8.862000 35.22500 ymin,ymax (A): -3.661000 34.03100 zmin,zma (A): 2.011000 49.61000 x,y,z range (A): 44.08700 37.69200 47.59900 scale (grids/A): 0.7479150 object centre (A): 13.18150 15.18500 25.81050 number of atom coordinates read : 2016 total number of charged atoms : 1882 net assigned charge : 5.931007 assigned positive charge : 304.4901 centred at (gu) : 90.14164 89.55283 91.15011 assigned negative charge : -298.5591 centred at (gu) : 89.94701 89.61217 91.20854 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7843 nv = 96 ne = 84 npr = 40381 no. pairs analyzed = 40381 no. exposed pairs = 2410 no. arc points = 16644 no. surface atoms = 823 nbur = 1193 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 611 mr = 4566 m= 7 mr = 142 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 0.2600000 number of dielectric boundary points 3753 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1503 ## 138 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 8200 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5322347E-07 7.1313671E-08 midg,1,midg; midg,igrid,midg 2.0587659E-07 5.3799379E-08 1,midg,midg; igrid,midg,midg -9.3255885E-08 3.4533687E-07 gauss-seidel spectral radius is 0.9906685 estimated iterations to convergence 84 setup time was (sec) 0.5100000 now iterating at: 06:09:22 rms-change max change #iterations 0.2479558 31.47314 at 10iterations 3.4374222E-02 4.241943 at 20iterations 4.9570305E-03 0.6486206 at 30iterations 8.0921926E-04 0.1084328 at 40iterations 1.8283474E-04 2.1309853E-02 at 50iterations finished qdiffx linear iterations at : 06:09:25 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 1.8283474E-04 2.1309853E-02 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 06:09:26 4.352u 0.393s 0:05.22 90.8% 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 06:09:26 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2016 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.243745 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): -8.862000 35.22500 ymin,ymax (A): -3.661000 34.03100 zmin,zma (A): 2.011000 49.61000 x,y,z range (A): 44.08700 37.69200 47.59900 scale (grids/A): 2.243745 object centre (A): 13.18150 15.18500 25.81050 number of atom coordinates read : 2016 total number of charged atoms : 1882 net assigned charge : 5.931007 assigned positive charge : 304.4901 centred at (gu) : 90.42503 88.65865 93.45052 assigned negative charge : -298.5591 centred at (gu) : 89.84126 88.83644 93.62582 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 82137 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16644 grid for indexing accessible points = 1.400000 m= 35570 mr = 58781 m= 8270 mr = 27649 m= 932 mr = 5834 m= 27 mr = 539 m= 0 mr = 7 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 34126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 14986 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) : 0.7479150 object centre at (A) : 13.18150 15.18500 25.81050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1425941E-02 6.1109536E-03 midg,1,midg; midg,igrid,midg 4.1792572E-02 1.0000780E-02 1,midg,midg; igrid,midg,midg 3.1166885E-02 6.5305121E-02 gauss-seidel spectral radius is 0.9989316 estimated iterations to convergence 242 setup time was (sec) 1.000000 now iterating at: 06:09:28 rms-change max change #iterations 4.959291 212.9371 at 10iterations 2.542351 80.98927 at 20iterations 1.302330 36.22771 at 30iterations 0.6671695 19.56821 at 40iterations 0.3435953 9.315859 at 50iterations 0.1761514 4.819273 at 60iterations 9.0331450E-02 2.528122 at 70iterations 4.6124354E-02 1.268343 at 80iterations 2.3749718E-02 0.6469588 at 90iterations 1.2306817E-02 0.3663025 at 100iterations 6.3665728E-03 0.2070236 at 110iterations 3.3196034E-03 9.7299576E-02 at 120iterations finished qdiffx linear iterations at : 06:09:37 total time elapsed so far: 10.52000 # loops : 120 mean,max change (kT/e) : 3.3196034E-03 9.7299576E-02 energy calculations done at 10.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.69000 DelPhi exited at 06:09:38 10.692u 0.436s 0:11.42 97.3% 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 Tue Oct 11 2011 at 06:09:38 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2016 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.365617 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): -8.862000 35.22500 ymin,ymax (A): -3.661000 34.03100 zmin,zma (A): 2.011000 49.61000 x,y,z range (A): 44.08700 37.69200 47.59900 scale (grids/A): 3.365617 object centre (A): 13.18150 15.18500 25.81050 number of atom coordinates read : 2016 total number of charged atoms : 1882 net assigned charge : 5.931007 assigned positive charge : 304.4901 centred at (gu) : 90.63765 87.98795 95.17592 assigned negative charge : -298.5591 centred at (gu) : 89.76172 88.25474 95.43880 start vw surface at 0.1000000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 188967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16644 grid for indexing accessible points = 1.400000 m= 106988 mr = 140808 m= 48408 mr = 90251 m= 16174 mr = 40685 m= 3766 mr = 13064 m= 586 mr = 2840 m= 21 mr = 426 m= 0 mr = 10 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.170000 number of dielectric boundary points 76826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 15056 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) : 2.243745 object centre at (A) : 13.18150 15.18500 25.81050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3764307 -3.5222977E-02 midg,1,midg; midg,igrid,midg 0.3148930 6.1215866E-02 1,midg,midg; igrid,midg,midg 0.4689092 0.4436637 gauss-seidel spectral radius is 0.9993204 estimated iterations to convergence 303 setup time was (sec) 2.510000 now iterating at: 06:09:41 rms-change max change #iterations 10.73630 309.0285 at 10iterations 6.431601 139.3424 at 20iterations 3.841754 68.94247 at 30iterations 2.290480 40.16906 at 40iterations 1.361817 25.11549 at 50iterations 0.8073503 15.13121 at 60iterations 0.4791788 9.484386 at 70iterations 0.2836748 5.029642 at 80iterations 0.1681473 2.840555 at 90iterations 9.9460654E-02 1.623997 at 100iterations 5.9039384E-02 0.9441690 at 110iterations 3.4982890E-02 0.5565376 at 120iterations 2.0966781E-02 0.3844490 at 130iterations 1.2677867E-02 0.2241783 at 140iterations 7.8386106E-03 0.1441574 at 150iterations 5.0298893E-03 8.7432861E-02 at 160iterations 3.3650436E-03 6.1347961E-02 at 170iterations 2.3935591E-03 4.3525696E-02 at 180iterations finished qdiffx linear iterations at : 06:09:57 total time elapsed so far: 18.53000 # loops : 180 mean,max change (kT/e) : 2.3935591E-03 4.3525696E-02 energy calculations done at 18.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.70000 DelPhi exited at 06:09:57 18.708u 0.475s 0:19.64 97.6% 0+0k 0+0io 0pf+0w