Mon Oct 10 14:21:18 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 14:21:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2852 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6176159 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): 2.601000 57.10400 ymin,ymax (A): 2.363000 52.60600 zmin,zma (A): 6.710000 64.35100 x,y,z range (A): 54.50300 50.24300 57.64100 scale (grids/A): 0.6176159 object centre (A): 29.85250 27.48450 35.53050 number of atom coordinates read : 2852 total number of charged atoms : 2715 net assigned charge : 8.000020 assigned positive charge : 420.7133 centred at (gu) : 90.57386 89.28871 90.19855 assigned negative charge : -412.7143 centred at (gu) : 90.58546 89.19160 90.13570 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7148 nv = 96 ne = 84 npr = 57959 no. pairs analyzed = 57959 no. exposed pairs = 3628 no. arc points = 25288 no. surface atoms = 1229 nbur = 1623 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 344 mr = 3774 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.3900000 number of dielectric boundary points 3695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2496 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8844 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7944833E-09 1.0598645E-08 midg,1,midg; midg,igrid,midg -5.7360150E-10 1.0585354E-08 1,midg,midg; igrid,midg,midg 6.0121002E-09 5.9527587E-09 gauss-seidel spectral radius is 0.9864484 estimated iterations to convergence 70 setup time was (sec) 0.6800000 now iterating at: 14:21:19 rms-change max change #iterations 0.1282176 19.68121 at 10iterations 1.1562679E-02 1.476472 at 20iterations 1.0676160E-03 0.1793976 at 30iterations 9.7009703E-05 1.3811111E-02 at 40iterations 9.0697231E-06 1.3103485E-03 at 50iterations finished qdiffx linear iterations at : 14:21:23 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 9.0697231E-06 1.3103485E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 14:21:23 4.248u 0.202s 0:04.73 93.8% 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 14:21:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2852 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.852848 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): 2.601000 57.10400 ymin,ymax (A): 2.363000 52.60600 zmin,zma (A): 6.710000 64.35100 x,y,z range (A): 54.50300 50.24300 57.64100 scale (grids/A): 1.852848 object centre (A): 29.85250 27.48450 35.53050 number of atom coordinates read : 2852 total number of charged atoms : 2715 net assigned charge : 8.000020 assigned positive charge : 420.7133 centred at (gu) : 91.72066 87.86551 90.59443 assigned negative charge : -412.7143 centred at (gu) : 91.75631 87.57442 90.40687 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 78146 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25288 grid for indexing accessible points = 1.400000 m= 25366 mr = 53376 m= 3386 mr = 17625 m= 158 mr = 1844 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 212 time to turn everything in is 0.7200000 number of dielectric boundary points 34178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 21249 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) : 0.6176159 object centre at (A) : 29.85250 27.48450 35.53050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8476555E-03 2.0665670E-02 midg,1,midg; midg,igrid,midg 5.8257701E-03 2.5830083E-02 1,midg,midg; igrid,midg,midg 1.3691932E-02 1.2762558E-02 gauss-seidel spectral radius is 0.9985876 estimated iterations to convergence 211 setup time was (sec) 1.070000 now iterating at: 14:21:25 rms-change max change #iterations 4.172482 192.3846 at 10iterations 1.928959 73.86937 at 20iterations 0.8890415 28.74232 at 30iterations 0.4105975 13.68662 at 40iterations 0.1898389 6.051576 at 50iterations 8.7517083E-02 2.749844 at 60iterations 4.0430322E-02 1.281542 at 70iterations 1.8743509E-02 0.5957990 at 80iterations 8.6564515E-03 0.2787256 at 90iterations 4.0081921E-03 0.1293650 at 100iterations 1.8602771E-03 5.9486389E-02 at 110iterations 8.6029462E-04 2.7414322E-02 at 120iterations finished qdiffx linear iterations at : 14:21:33 total time elapsed so far: 9.280000 # loops : 120 mean,max change (kT/e) : 8.6029462E-04 2.7414322E-02 energy calculations done at 9.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.520000 DelPhi exited at 14:21:33 9.524u 0.240s 0:10.17 95.9% 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 Mon Oct 10 2011 at 14:21:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2852 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.779272 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): 2.601000 57.10400 ymin,ymax (A): 2.363000 52.60600 zmin,zma (A): 6.710000 64.35100 x,y,z range (A): 54.50300 50.24300 57.64100 scale (grids/A): 2.779272 object centre (A): 29.85250 27.48450 35.53050 number of atom coordinates read : 2852 total number of charged atoms : 2715 net assigned charge : 8.000020 assigned positive charge : 420.7133 centred at (gu) : 92.58073 86.79800 90.89173 assigned negative charge : -412.7143 centred at (gu) : 92.63452 86.36151 90.61021 start vw surface at 0.2100000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 181127 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25288 grid for indexing accessible points = 1.400000 m= 84845 mr = 130022 m= 27171 mr = 67611 m= 5752 mr = 20533 m= 696 mr = 4012 m= 34 mr = 350 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 745 time to turn everything in is 1.820000 number of dielectric boundary points 77084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 21718 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) : 1.852848 object centre at (A) : 29.85250 27.48450 35.53050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2643379 0.1275557 midg,1,midg; midg,igrid,midg 7.1661599E-02 0.3044849 1,midg,midg; igrid,midg,midg 0.2152754 0.2565946 gauss-seidel spectral radius is 0.9992548 estimated iterations to convergence 289 setup time was (sec) 2.200000 now iterating at: 14:21:36 rms-change max change #iterations 9.998444 284.0401 at 10iterations 5.865865 124.3925 at 20iterations 3.409405 79.01392 at 30iterations 1.979049 56.00220 at 40iterations 1.143524 25.05924 at 50iterations 0.6586734 12.26376 at 60iterations 0.3799690 7.468262 at 70iterations 0.2187107 4.487331 at 80iterations 0.1256756 2.387856 at 90iterations 7.2116129E-02 1.260003 at 100iterations 4.1373249E-02 0.7437191 at 110iterations 2.3795817E-02 0.4584074 at 120iterations 1.3648693E-02 0.2400093 at 130iterations 7.8350091E-03 0.1384430 at 140iterations 4.4857888E-03 8.0469131E-02 at 150iterations 2.5741325E-03 4.5295715E-02 at 160iterations 1.4773828E-03 2.6762009E-02 at 170iterations 8.4874290E-04 1.5429497E-02 at 180iterations finished qdiffx linear iterations at : 14:21:49 total time elapsed so far: 15.33000 # loops : 180 mean,max change (kT/e) : 8.4874290E-04 1.5429497E-02 energy calculations done at 15.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.57000 DelPhi exited at 14:21:50 15.569u 0.249s 0:16.30 96.9% 0+0k 0+0io 0pf+0w