Tue Oct 11 05:49:27 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 05:49:27 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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: 0.7408024 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): 25.63100 72.61900 ymin,ymax (A): -18.38900 29.66700 zmin,zma (A): 4.004000 45.95000 x,y,z range (A): 46.98801 48.05600 41.94600 scale (grids/A): 0.7408024 object centre (A): 49.12500 5.639000 24.97700 number of atom coordinates read : 2290 total number of charged atoms : 1963 net assigned charge : 5.945010 assigned positive charge : 319.5460 centred at (gu) : 88.98720 90.54844 90.26922 assigned negative charge : -313.6011 centred at (gu) : 89.11755 90.47723 90.34685 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7917 nv = 96 ne = 84 npr = 42142 no. pairs analyzed = 42142 no. exposed pairs = 2562 no. arc points = 17397 no. surface atoms = 880 nbur = 1410 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 588 mr = 4637 m= 2 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1561 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8323 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7401777E-07 2.6891403E-08 midg,1,midg; midg,igrid,midg 2.9858100E-08 1.9535473E-07 1,midg,midg; igrid,midg,midg 2.8433391E-07 -2.2432557E-08 gauss-seidel spectral radius is 0.9904952 estimated iterations to convergence 83 setup time was (sec) 0.3700000 now iterating at: 05:49:28 rms-change max change #iterations 0.2473865 31.95069 at 10iterations 3.3862699E-02 3.984253 at 20iterations 5.0503449E-03 0.7201767 at 30iterations 9.8300807E-04 0.1182785 at 40iterations 2.7854703E-04 3.1013489E-02 at 50iterations finished qdiffx linear iterations at : 05:49:31 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.7854703E-04 3.1013489E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 05:49:31 3.373u 0.161s 0:03.94 89.5% 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 Tue Oct 11 2011 at 05:49:31 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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: 2.222407 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): 25.63100 72.61900 ymin,ymax (A): -18.38900 29.66700 zmin,zma (A): 4.004000 45.95000 x,y,z range (A): 46.98801 48.05600 41.94600 scale (grids/A): 2.222407 object centre (A): 49.12500 5.639000 24.97700 number of atom coordinates read : 2290 total number of charged atoms : 1963 net assigned charge : 5.945010 assigned positive charge : 319.5460 centred at (gu) : 86.96170 91.64536 90.80760 assigned negative charge : -313.6011 centred at (gu) : 87.35274 91.43193 91.04072 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 83057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17397 grid for indexing accessible points = 1.400000 m= 34990 mr = 59579 m= 7427 mr = 26931 m= 824 mr = 5140 m= 30 mr = 421 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 34258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 15624 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) : 0.7408024 object centre at (A) : 49.12500 5.639000 24.97700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1928340E-02 3.3628616E-02 midg,1,midg; midg,igrid,midg 4.4412836E-02 4.3462992E-02 1,midg,midg; igrid,midg,midg 5.8241021E-02 -5.2917514E-02 gauss-seidel spectral radius is 0.9989203 estimated iterations to convergence 241 setup time was (sec) 0.6500000 now iterating at: 05:49:32 rms-change max change #iterations 5.024488 219.7741 at 10iterations 2.554677 80.47115 at 20iterations 1.305815 41.31370 at 30iterations 0.6663171 20.34426 at 40iterations 0.3405031 9.313835 at 50iterations 0.1741000 4.914960 at 60iterations 8.8932015E-02 2.298876 at 70iterations 4.5561213E-02 1.239311 at 80iterations 2.3498539E-02 0.7802691 at 90iterations 1.2200013E-02 0.3247604 at 100iterations 6.3843913E-03 0.2082520 at 110iterations 3.4174058E-03 9.9599838E-02 at 120iterations finished qdiffx linear iterations at : 05:49:39 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 3.4174058E-03 9.9599838E-02 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 05:49:40 7.904u 0.202s 0:08.38 96.6% 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 05:49:40 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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: 3.333611 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): 25.63100 72.61900 ymin,ymax (A): -18.38900 29.66700 zmin,zma (A): 4.004000 45.95000 x,y,z range (A): 46.98801 48.05600 41.94600 scale (grids/A): 3.333611 object centre (A): 49.12500 5.639000 24.97700 number of atom coordinates read : 2290 total number of charged atoms : 1963 net assigned charge : 5.945010 assigned positive charge : 319.5460 centred at (gu) : 85.44253 92.46807 91.21141 assigned negative charge : -313.6011 centred at (gu) : 86.02914 92.14792 91.56110 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 190953 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17397 grid for indexing accessible points = 1.400000 m= 107050 mr = 142687 m= 46319 mr = 90109 m= 14499 mr = 38562 m= 3364 mr = 11423 m= 482 mr = 2444 m= 43 mr = 326 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 77137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 15700 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) : 2.222407 object centre at (A) : 49.12500 5.639000 24.97700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1802001E-02 0.2657881 midg,1,midg; midg,igrid,midg 0.3793793 0.2935099 1,midg,midg; igrid,midg,midg 0.5340319 -0.6053596 gauss-seidel spectral radius is 0.9993197 estimated iterations to convergence 302 setup time was (sec) 1.560000 now iterating at: 05:49:41 rms-change max change #iterations 10.95139 266.0712 at 10iterations 6.548412 143.1155 at 20iterations 3.908870 88.25014 at 30iterations 2.325315 43.22286 at 40iterations 1.387460 26.89934 at 50iterations 0.8231925 15.49093 at 60iterations 0.4874568 8.395401 at 70iterations 0.2886759 5.419044 at 80iterations 0.1708952 2.894659 at 90iterations 0.1011580 1.666138 at 100iterations 6.0064685E-02 0.9740601 at 110iterations 3.5803318E-02 0.5811708 at 120iterations 2.1570392E-02 0.3669586 at 130iterations 1.3198098E-02 0.2286034 at 140iterations 8.3331550E-03 0.1513863 at 150iterations 5.5106846E-03 9.6997261E-02 at 160iterations 3.8423860E-03 6.2339783E-02 at 170iterations 2.8534343E-03 4.5913696E-02 at 180iterations finished qdiffx linear iterations at : 05:49:53 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 2.8534343E-03 4.5913696E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 05:49:54 13.169u 0.206s 0:13.89 96.1% 0+0k 0+0io 0pf+0w