Tue Nov 22 14:12:02 PST 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 Nov 22 2011 at 14:12:04 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6396205 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): -5.277000 34.71600 ymin,ymax (A): -3.616000 47.62100 zmin,zma (A): -24.43000 31.22800 x,y,z range (A): 39.99300 51.23700 55.65800 scale (grids/A): 0.6396205 object centre (A): 14.71950 22.00250 3.399000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 90.65284 92.86518 90.18874 assigned negative charge : -288.0262 centred at (gu) : 90.76023 92.98865 90.12447 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5518 nv = 96 ne = 84 npr = 40207 no. pairs analyzed = 40207 no. exposed pairs = 2461 no. arc points = 17428 no. surface atoms = 840 nbur = 1124 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 281 mr = 3085 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1807 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6536 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.5743006E-10 1.0509011E-08 midg,1,midg; midg,igrid,midg 8.1963005E-09 -1.1483624E-08 1,midg,midg; igrid,midg,midg 1.1899649E-08 -5.2582614E-09 gauss-seidel spectral radius is 0.9872801 estimated iterations to convergence 72 setup time was (sec) 0.4200000 now iterating at: 14:12:05 rms-change max change #iterations 0.1244807 21.44889 at 10iterations 1.2324938E-02 1.959532 at 20iterations 1.2053967E-03 0.1728578 at 30iterations 1.1922560E-04 1.8125534E-02 at 40iterations 1.1731201E-05 1.7013550E-03 at 50iterations finished qdiffx linear iterations at : 14:12:15 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 1.1731201E-05 1.7013550E-03 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.910000 DelPhi exited at 14:12:16 3.909u 0.276s 0:12.65 32.9% 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 Nov 22 2011 at 14:12:20 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.918862 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): -5.277000 34.71600 ymin,ymax (A): -3.616000 47.62100 zmin,zma (A): -24.43000 31.22800 x,y,z range (A): 39.99300 51.23700 55.65800 scale (grids/A): 1.918862 object centre (A): 14.71950 22.00250 3.399000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 91.95863 98.59570 90.56609 assigned negative charge : -288.0262 centred at (gu) : 92.28088 98.96619 90.37338 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 59069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17428 grid for indexing accessible points = 1.400000 m= 21810 mr = 40734 m= 3376 mr = 16853 m= 181 mr = 2221 m= 0 mr = 69 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1035 time to turn everything in is 0.3200000 number of dielectric boundary points 24559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14415 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) : 0.6396205 object centre at (A) : 14.71950 22.00250 3.399000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6561774E-02 1.3383618E-02 midg,1,midg; midg,igrid,midg 2.9192852E-02 -9.0832850E-03 1,midg,midg; igrid,midg,midg 6.2050973E-03 -5.4526096E-03 gauss-seidel spectral radius is 0.9985747 estimated iterations to convergence 210 setup time was (sec) 0.5800000 now iterating at: 14:12:25 rms-change max change #iterations 3.672309 147.4612 at 10iterations 1.687536 66.42154 at 20iterations 0.7795238 28.64466 at 30iterations 0.3604502 13.37088 at 40iterations 0.1649019 5.698093 at 50iterations 7.6141246E-02 2.655668 at 60iterations 3.4944650E-02 1.258081 at 70iterations 1.6126964E-02 0.5575109 at 80iterations 7.4040270E-03 0.2645321 at 90iterations 3.4251830E-03 0.1209326 at 100iterations 1.5700618E-03 5.6104660E-02 at 110iterations 7.2506495E-04 2.4887085E-02 at 120iterations finished qdiffx linear iterations at : 14:12:51 total time elapsed so far: 8.710000 # loops : 120 mean,max change (kT/e) : 7.2506495E-04 2.4887085E-02 energy calculations done at 8.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.850000 DelPhi exited at 14:12:53 8.853u 0.245s 0:33.51 27.1% 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 Nov 22 2011 at 14:12:55 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.878292 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): -5.277000 34.71600 ymin,ymax (A): -3.616000 47.62100 zmin,zma (A): -24.43000 31.22800 x,y,z range (A): 39.99300 51.23700 55.65800 scale (grids/A): 2.878292 object centre (A): 14.71950 22.00250 3.399000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 92.93788 102.8935 90.84900 assigned negative charge : -288.0262 centred at (gu) : 93.42139 103.4494 90.56016 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 136225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17428 grid for indexing accessible points = 1.400000 m= 70094 mr = 98454 m= 26398 mr = 58352 m= 6137 mr = 22131 m= 732 mr = 4774 m= 36 mr = 528 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 3806 time to turn everything in is 0.7900000 number of dielectric boundary points 55370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 14655 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) : 1.918862 object centre at (A) : 14.71950 22.00250 3.399000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.063209 3.0000051E-02 midg,1,midg; midg,igrid,midg 0.3126805 -0.1157964 1,midg,midg; igrid,midg,midg 3.4727596E-02 -3.1855606E-02 gauss-seidel spectral radius is 0.9992286 estimated iterations to convergence 284 setup time was (sec) 1.040000 now iterating at: 14:13:02 rms-change max change #iterations 8.564968 332.9783 at 10iterations 4.901747 128.4452 at 20iterations 2.784956 60.26662 at 30iterations 1.584536 31.42282 at 40iterations 0.8978901 17.28585 at 50iterations 0.5093045 10.77577 at 60iterations 0.2892682 5.894291 at 70iterations 0.1638844 3.206052 at 80iterations 9.2893556E-02 1.942990 at 90iterations 5.2537389E-02 1.036256 at 100iterations 2.9816277E-02 0.6032715 at 110iterations 1.6900819E-02 0.3527913 at 120iterations 9.5761279E-03 0.2012212 at 130iterations 5.4369099E-03 0.1057949 at 140iterations 3.0725440E-03 6.0766220E-02 at 150iterations 1.7456000E-03 3.8375854E-02 at 160iterations 9.9015131E-04 2.1353722E-02 at 170iterations 5.5987563E-04 1.1413574E-02 at 180iterations finished qdiffx linear iterations at : 14:13:26 total time elapsed so far: 13.59000 # loops : 180 mean,max change (kT/e) : 5.5987563E-04 1.1413574E-02 energy calculations done at 13.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.72000 DelPhi exited at 14:13:30 13.726u 0.254s 0:35.02 39.8% 0+0k 0+0io 0pf+0w