Tue Oct 11 05:26:53 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 05:26:53 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2237 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.6877234 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): 19.95000 63.24800 ymin,ymax (A): -3.483000 33.69500 zmin,zma (A): 20.13600 71.90100 x,y,z range (A): 43.29800 37.17800 51.76500 scale (grids/A): 0.6877234 object centre (A): 41.59900 15.10600 46.01850 number of atom coordinates read : 2237 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 311.5670 centred at (gu) : 90.17876 89.66339 89.37261 assigned negative charge : -304.5422 centred at (gu) : 90.35470 89.68032 89.35390 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6608 nv = 96 ne = 84 npr = 40627 no. pairs analyzed = 40627 no. exposed pairs = 2546 no. arc points = 17186 no. surface atoms = 871 nbur = 1366 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 400 mr = 3755 m= 6 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1686 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7465 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5105067E-08 3.7739660E-08 midg,1,midg; midg,igrid,midg 4.4927202E-08 2.9710870E-08 1,midg,midg; igrid,midg,midg 8.6779863E-08 -1.8864561E-08 gauss-seidel spectral radius is 0.9889819 estimated iterations to convergence 78 setup time was (sec) 0.4600000 now iterating at: 05:26:54 rms-change max change #iterations 0.1719807 23.26003 at 10iterations 2.0552834E-02 3.015886 at 20iterations 2.7358050E-03 0.3736582 at 30iterations 5.0701352E-04 6.3888550E-02 at 40iterations 1.3326474E-04 1.6225815E-02 at 50iterations finished qdiffx linear iterations at : 05:26:56 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 1.3326474E-04 1.6225815E-02 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 05:26:57 3.149u 0.181s 0:03.86 86.0% 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 Tue Oct 11 2011 at 05:26:57 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2237 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.063170 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): 19.95000 63.24800 ymin,ymax (A): -3.483000 33.69500 zmin,zma (A): 20.13600 71.90100 x,y,z range (A): 43.29800 37.17800 51.76500 scale (grids/A): 2.063170 object centre (A): 41.59900 15.10600 46.01850 number of atom coordinates read : 2237 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 311.5670 centred at (gu) : 90.53645 88.99011 88.11761 assigned negative charge : -304.5422 centred at (gu) : 91.06416 89.04102 88.06161 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17186 grid for indexing accessible points = 1.400000 m= 28230 mr = 49684 m= 5346 mr = 21480 m= 450 mr = 3542 m= 7 mr = 213 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 29253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15273 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) : 0.6877234 object centre at (A) : 41.59900 15.10600 46.01850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4527579E-02 3.9753202E-02 midg,1,midg; midg,igrid,midg 2.1732643E-02 1.0451043E-02 1,midg,midg; igrid,midg,midg 3.7166465E-02 7.4651893E-03 gauss-seidel spectral radius is 0.9987694 estimated iterations to convergence 226 setup time was (sec) 0.8200000 now iterating at: 05:26:58 rms-change max change #iterations 4.340578 199.5942 at 10iterations 2.123774 70.18944 at 20iterations 1.027845 34.10466 at 30iterations 0.5052912 15.47164 at 40iterations 0.2467126 8.714734 at 50iterations 0.1200233 3.731659 at 60iterations 5.8731236E-02 1.705330 at 70iterations 2.8774258E-02 0.9416332 at 80iterations 1.4198848E-02 0.4776993 at 90iterations 7.0034773E-03 0.2172108 at 100iterations 3.5049974E-03 0.1219168 at 110iterations 1.8097711E-03 5.8807373E-02 at 120iterations finished qdiffx linear iterations at : 05:27:04 total time elapsed so far: 7.060000 # loops : 120 mean,max change (kT/e) : 1.8097711E-03 5.8807373E-02 energy calculations done at 7.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.240000 DelPhi exited at 05:27:05 7.243u 0.209s 0:07.73 96.2% 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 05:27:05 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2237 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.094755 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): 19.95000 63.24800 ymin,ymax (A): -3.483000 33.69500 zmin,zma (A): 20.13600 71.90100 x,y,z range (A): 43.29800 37.17800 51.76500 scale (grids/A): 3.094755 object centre (A): 41.59900 15.10600 46.01850 number of atom coordinates read : 2237 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 311.5670 centred at (gu) : 90.80466 88.48515 87.17643 assigned negative charge : -304.5422 centred at (gu) : 91.59635 88.56169 87.09245 start vw surface at 0.1300000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 161638 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17186 grid for indexing accessible points = 1.400000 m= 88095 mr = 119750 m= 35497 mr = 73303 m= 10021 mr = 29187 m= 1883 mr = 7819 m= 162 mr = 1346 m= 2 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.720000 number of dielectric boundary points 65810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 15416 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) : 2.063170 object centre at (A) : 41.59900 15.10600 46.01850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3356249 0.2701708 midg,1,midg; midg,igrid,midg 0.1895459 8.3809413E-02 1,midg,midg; igrid,midg,midg 0.3121153 0.2221677 gauss-seidel spectral radius is 0.9992792 estimated iterations to convergence 294 setup time was (sec) 2.020000 now iterating at: 05:27:07 rms-change max change #iterations 9.805187 484.9172 at 10iterations 5.800660 180.4358 at 20iterations 3.406100 88.22186 at 30iterations 1.998740 41.86858 at 40iterations 1.167870 23.16873 at 50iterations 0.6835436 12.93269 at 60iterations 0.3996361 7.886803 at 70iterations 0.2325812 5.276925 at 80iterations 0.1356039 2.536611 at 90iterations 7.9091340E-02 1.529881 at 100iterations 4.6222668E-02 0.8578755 at 110iterations 2.7171554E-02 0.5180016 at 120iterations 1.6100880E-02 0.3174591 at 130iterations 9.6806744E-03 0.1897316 at 140iterations 5.9869438E-03 0.1103745 at 150iterations 3.8653605E-03 7.0976257E-02 at 160iterations 2.6481471E-03 4.8450470E-02 at 170iterations 1.9194011E-03 3.3401489E-02 at 180iterations finished qdiffx linear iterations at : 05:27:18 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 1.9194011E-03 3.3401489E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 05:27:18 12.581u 0.248s 0:13.35 96.0% 0+0k 0+0io 0pf+0w