Tue Oct 11 03:34:53 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 03:34:53 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 = 2349 !!! WARNING: HIR 217 has a net charge of 0.5140 !!! WARNING: ASP 243 has a net charge of -2.0000 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: 0.6669289 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): -1.333000 50.51600 ymin,ymax (A): 10.47100 62.90900 zmin,zma (A): 6.349000 59.72800 x,y,z range (A): 51.84900 52.43800 53.37900 scale (grids/A): 0.6669289 object centre (A): 24.59150 36.69000 33.03850 number of atom coordinates read : 2349 total number of charged atoms : 2253 net assigned charge : -5.485981 assigned positive charge : 351.6292 centred at (gu) : 90.02057 89.52866 90.29343 assigned negative charge : -357.1157 centred at (gu) : 90.10486 89.51113 90.44128 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7007 nv = 96 ne = 84 npr = 47894 no. pairs analyzed = 47894 no. exposed pairs = 3077 no. arc points = 21766 no. surface atoms = 1035 nbur = 1314 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 453 mr = 3689 m= 1 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3200000 number of dielectric boundary points 3688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2036 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8266 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4023263E-08 -5.2307364E-08 midg,1,midg; midg,igrid,midg -2.2474516E-08 -1.1705106E-08 1,midg,midg; igrid,midg,midg 1.4972187E-09 -3.5235036E-08 gauss-seidel spectral radius is 0.9883294 estimated iterations to convergence 76 setup time was (sec) 0.5900000 now iterating at: 03:34:53 rms-change max change #iterations 0.1677423 22.74331 at 10iterations 1.8078795E-02 2.463227 at 20iterations 1.9718041E-03 0.2726364 at 30iterations 2.1391785E-04 3.0965805E-02 at 40iterations 2.3355098E-05 3.1967163E-03 at 50iterations finished qdiffx linear iterations at : 03:34:57 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 2.3355098E-05 3.1967163E-03 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 03:34:57 4.036u 0.261s 0:04.74 90.5% 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 03:34:57 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 = 2349 !!! WARNING: HIR 217 has a net charge of 0.5140 !!! WARNING: ASP 243 has a net charge of -2.0000 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: 2.000787 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): -1.333000 50.51600 ymin,ymax (A): 10.47100 62.90900 zmin,zma (A): 6.349000 59.72800 x,y,z range (A): 51.84900 52.43800 53.37900 scale (grids/A): 2.000787 object centre (A): 24.59150 36.69000 33.03850 number of atom coordinates read : 2349 total number of charged atoms : 2253 net assigned charge : -5.485981 assigned positive charge : 351.6292 centred at (gu) : 90.06114 88.58556 90.87984 assigned negative charge : -357.1157 centred at (gu) : 90.31424 88.53328 91.32352 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 73867 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21766 grid for indexing accessible points = 1.400000 m= 28370 mr = 49415 m= 5687 mr = 20981 m= 478 mr = 3735 m= 10 mr = 212 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 491 time to turn everything in is 0.7000000 number of dielectric boundary points 34069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 90 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 17820 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) : 0.6669289 object centre at (A) : 24.59150 36.69000 33.03850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9783010E-02 -9.7452670E-02 midg,1,midg; midg,igrid,midg -1.4650612E-03 1.4108906E-02 1,midg,midg; igrid,midg,midg 4.6540014E-03 1.6063405E-03 gauss-seidel spectral radius is 0.9987411 estimated iterations to convergence 223 setup time was (sec) 0.9900000 now iterating at: 03:34:59 rms-change max change #iterations 4.464467 176.3263 at 10iterations 2.142370 78.17143 at 20iterations 1.034568 32.80470 at 30iterations 0.4962712 17.33242 at 40iterations 0.2394780 7.852402 at 50iterations 0.1153264 3.778053 at 60iterations 5.5401392E-02 1.828127 at 70iterations 2.6795018E-02 0.8022404 at 80iterations 1.2902549E-02 0.3745170 at 90iterations 6.2239077E-03 0.1969543 at 100iterations 3.0133482E-03 0.1005096 at 110iterations 1.4502010E-03 4.7578812E-02 at 120iterations finished qdiffx linear iterations at : 03:35:07 total time elapsed so far: 9.290000 # loops : 120 mean,max change (kT/e) : 1.4502010E-03 4.7578812E-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) 9.460000 DelPhi exited at 03:35:08 9.462u 0.297s 0:10.18 95.7% 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 03:35:08 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 = 2349 !!! WARNING: HIR 217 has a net charge of 0.5140 !!! WARNING: ASP 243 has a net charge of -2.0000 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: 3.001180 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): -1.333000 50.51600 ymin,ymax (A): 10.47100 62.90900 zmin,zma (A): 6.349000 59.72800 x,y,z range (A): 51.84900 52.43800 53.37900 scale (grids/A): 3.001180 object centre (A): 24.59150 36.69000 33.03850 number of atom coordinates read : 2349 total number of charged atoms : 2253 net assigned charge : -5.485981 assigned positive charge : 351.6292 centred at (gu) : 90.09169 87.87822 91.31966 assigned negative charge : -357.1157 centred at (gu) : 90.47145 87.79986 91.98528 start vw surface at 0.1500000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 170134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21766 grid for indexing accessible points = 1.400000 m= 87166 mr = 119613 m= 36712 mr = 70875 m= 10736 mr = 29895 m= 2007 mr = 8231 m= 168 mr = 1400 m= 4 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 1789 time to turn everything in is 1.800000 number of dielectric boundary points 76827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 18024 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) : 2.000787 object centre at (A) : 24.59150 36.69000 33.03850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4191524 -1.051449 midg,1,midg; midg,igrid,midg -1.5917080E-03 0.1797404 1,midg,midg; igrid,midg,midg 8.5753471E-02 0.2618792 gauss-seidel spectral radius is 0.9992889 estimated iterations to convergence 296 setup time was (sec) 2.130000 now iterating at: 03:35:10 rms-change max change #iterations 10.13287 502.1079 at 10iterations 5.905471 123.0435 at 20iterations 3.440535 73.86597 at 30iterations 1.999241 39.34190 at 40iterations 1.165096 20.23793 at 50iterations 0.6762738 11.87889 at 60iterations 0.3922742 7.109121 at 70iterations 0.2274520 4.312785 at 80iterations 0.1317116 2.201521 at 90iterations 7.6546431E-02 1.435867 at 100iterations 4.4424102E-02 0.7444439 at 110iterations 2.5739657E-02 0.4607573 at 120iterations 1.4923749E-02 0.2495041 at 130iterations 8.6560398E-03 0.1505280 at 140iterations 5.0213947E-03 8.2153320E-02 at 150iterations 2.9151067E-03 4.7461510E-02 at 160iterations 1.6949901E-03 2.9296875E-02 at 170iterations 9.8403741E-04 1.8767357E-02 at 180iterations finished qdiffx linear iterations at : 03:35:24 total time elapsed so far: 15.86000 # loops : 180 mean,max change (kT/e) : 9.8403741E-04 1.8767357E-02 energy calculations done at 15.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.04000 DelPhi exited at 03:35:25 16.039u 0.314s 0:16.84 97.0% 0+0k 0+0io 0pf+0w