Mon Oct 10 14:00:19 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 Mon Oct 10 2011 at 14:00:19 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2578 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 702 has a net charge of 1.4000 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: 0.6193243 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): -32.22800 17.50100 ymin,ymax (A): -23.51900 22.33800 zmin,zma (A): -12.44000 45.04200 x,y,z range (A): 49.72900 45.85700 57.48200 scale (grids/A): 0.6193243 object centre (A): -7.363501 -0.5904999 16.30100 number of atom coordinates read : 2578 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.72453 89.36408 89.63105 assigned negative charge : -387.4045 centred at (gu) : 88.62893 89.41451 89.50235 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6341 nv = 96 ne = 84 npr = 54427 no. pairs analyzed = 54427 no. exposed pairs = 2988 no. arc points = 21422 no. surface atoms = 1005 nbur = 1573 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 311 mr = 3487 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.3500000 number of dielectric boundary points 3128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2176 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8050 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6862932E-09 1.0593355E-08 midg,1,midg; midg,igrid,midg 7.4910007E-09 -9.0046590E-12 1,midg,midg; igrid,midg,midg -4.0902868E-09 7.1067552E-09 gauss-seidel spectral radius is 0.9864917 estimated iterations to convergence 70 setup time was (sec) 0.6100000 now iterating at: 14:00:20 rms-change max change #iterations 0.1219610 20.92231 at 10iterations 1.1118280E-02 1.695557 at 20iterations 1.0157153E-03 0.1609087 at 30iterations 9.6232958E-05 1.3687134E-02 at 40iterations 8.7450844E-06 1.3160706E-03 at 50iterations finished qdiffx linear iterations at : 14:00:23 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 8.7450844E-06 1.3160706E-03 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 14:00:24 4.052u 0.274s 0:05.03 85.8% 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 Mon Oct 10 2011 at 14:00:24 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2578 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 702 has a net charge of 1.4000 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: 1.857973 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): -32.22800 17.50100 ymin,ymax (A): -23.51900 22.33800 zmin,zma (A): -12.44000 45.04200 x,y,z range (A): 49.72900 45.85700 57.48200 scale (grids/A): 1.857973 object centre (A): -7.363501 -0.5904999 16.30100 number of atom coordinates read : 2578 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 86.17304 88.09162 88.89250 assigned negative charge : -387.4045 centred at (gu) : 85.88641 88.24337 88.50681 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 69036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21422 grid for indexing accessible points = 1.400000 m= 23629 mr = 47963 m= 3500 mr = 17297 m= 185 mr = 2229 m= 3 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 3597 time to turn everything in is 0.6200000 number of dielectric boundary points 28800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19227 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) : 0.6193243 object centre at (A) : -7.363501 -0.5904999 16.30100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8289058E-02 2.9573577E-02 midg,1,midg; midg,igrid,midg 1.2752984E-02 8.1100629E-04 1,midg,midg; igrid,midg,midg -6.0245711E-03 3.5366561E-02 gauss-seidel spectral radius is 0.9985608 estimated iterations to convergence 209 setup time was (sec) 0.9200000 now iterating at: 14:00:25 rms-change max change #iterations 4.031006 199.8819 at 10iterations 1.845919 60.75872 at 20iterations 0.8450003 35.71381 at 30iterations 0.3886060 13.99373 at 40iterations 0.1787504 5.850954 at 50iterations 8.2104705E-02 2.960767 at 60iterations 3.7750088E-02 1.183125 at 70iterations 1.7312359E-02 0.6557693 at 80iterations 7.9076784E-03 0.2514000 at 90iterations 3.6435954E-03 0.1222534 at 100iterations 1.6696629E-03 5.5339098E-02 at 110iterations 7.6839805E-04 2.4581909E-02 at 120iterations finished qdiffx linear iterations at : 14:00:33 total time elapsed so far: 9.160000 # loops : 120 mean,max change (kT/e) : 7.6839805E-04 2.4581909E-02 energy calculations done at 9.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.340000 DelPhi exited at 14:00:34 9.340u 0.294s 0:10.03 96.0% 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 Mon Oct 10 2011 at 14:00:34 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2578 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 702 has a net charge of 1.4000 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: 2.786959 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): -32.22800 17.50100 ymin,ymax (A): -23.51900 22.33800 zmin,zma (A): -12.44000 45.04200 x,y,z range (A): 49.72900 45.85700 57.48200 scale (grids/A): 2.786959 object centre (A): -7.363501 -0.5904999 16.30100 number of atom coordinates read : 2578 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 84.25938 87.13728 88.33867 assigned negative charge : -387.4045 centred at (gu) : 83.82965 87.36487 87.76015 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 160210 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21422 grid for indexing accessible points = 1.400000 m= 78362 mr = 116613 m= 26498 mr = 64172 m= 6227 mr = 21225 m= 867 mr = 4695 m= 37 mr = 587 m= 0 mr = 15 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 12930 time to turn everything in is 1.550000 number of dielectric boundary points 64894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 19630 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) : 1.857973 object centre at (A) : -7.363501 -0.5904999 16.30100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0384476E-02 0.4144671 midg,1,midg; midg,igrid,midg 0.1458868 -1.8475000E-02 1,midg,midg; igrid,midg,midg -5.6191117E-02 0.4598347 gauss-seidel spectral radius is 0.9992315 estimated iterations to convergence 285 setup time was (sec) 1.860000 now iterating at: 14:00:36 rms-change max change #iterations 9.440535 275.2401 at 10iterations 5.424982 110.7072 at 20iterations 3.099517 69.21736 at 30iterations 1.765206 40.82765 at 40iterations 1.003946 21.68372 at 50iterations 0.5720006 11.56463 at 60iterations 0.3246345 6.688927 at 70iterations 0.1844795 3.547387 at 80iterations 0.1047766 1.877038 at 90iterations 5.9692774E-02 1.095655 at 100iterations 3.3824608E-02 0.6474552 at 110iterations 1.9217601E-02 0.3710346 at 120iterations 1.0920147E-02 0.2067604 at 130iterations 6.2039271E-03 0.1208687 at 140iterations 3.5183497E-03 6.8492889E-02 at 150iterations 2.0006683E-03 3.9707661E-02 at 160iterations 1.1349849E-03 2.0620346E-02 at 170iterations 6.4511964E-04 1.2329102E-02 at 180iterations finished qdiffx linear iterations at : 14:00:50 total time elapsed so far: 15.31000 # loops : 180 mean,max change (kT/e) : 6.4511964E-04 1.2329102E-02 energy calculations done at 15.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.49000 DelPhi exited at 14:00:51 15.488u 0.302s 0:16.65 94.7% 0+0k 0+0io 0pf+0w