Sat Oct 15 12:07:11 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 Sat Oct 15 2011 at 12:07:11 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3293 !!! WARNING: HIR 83 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5720621 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): -15.88100 40.22800 ymin,ymax (A): 16.91800 76.95700 zmin,zma (A): 25.37600 87.60700 x,y,z range (A): 56.10900 60.03900 62.23100 scale (grids/A): 0.5720621 object centre (A): 12.17350 46.93750 56.49150 number of atom coordinates read : 3293 total number of charged atoms : 3152 net assigned charge : 12.24003 assigned positive charge : 489.9337 centred at (gu) : 89.89341 90.04617 90.73367 assigned negative charge : -477.6953 centred at (gu) : 89.76012 90.08863 90.90176 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7416 nv = 96 ne = 84 npr = 64369 no. pairs analyzed = 64369 no. exposed pairs = 4261 no. arc points = 30966 no. surface atoms = 1420 nbur = 1873 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 334 mr = 3842 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2400000 number of dielectric boundary points 3879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3100 ## 329 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9292 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2391117E-09 -1.2795979E-09 midg,1,midg; midg,igrid,midg 2.7899079E-09 1.2947805E-09 1,midg,midg; igrid,midg,midg -4.1218784E-10 4.3209383E-09 gauss-seidel spectral radius is 0.9842693 estimated iterations to convergence 66 setup time was (sec) 0.4600000 now iterating at: 12:07:11 rms-change max change #iterations 0.1000192 14.89904 at 10iterations 7.4476823E-03 1.168755 at 20iterations 5.8010576E-04 0.1008406 at 30iterations 4.9994167E-05 6.6680908E-03 at 40iterations 5.7039874E-06 7.0428848E-04 at 50iterations finished qdiffx linear iterations at : 12:07:16 total time elapsed so far: 3.810000 # loops : 50 mean,max change (kT/e) : 5.7039874E-06 7.0428848E-04 energy calculations done at 3.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.940000 DelPhi exited at 12:07:16 3.948u 0.258s 0:05.83 71.8% 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 Sat Oct 15 2011 at 12:07:16 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3293 !!! WARNING: HIR 83 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.716186 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): -15.88100 40.22800 ymin,ymax (A): 16.91800 76.95700 zmin,zma (A): 25.37600 87.60700 x,y,z range (A): 56.10900 60.03900 62.23100 scale (grids/A): 1.716186 object centre (A): 12.17350 46.93750 56.49150 number of atom coordinates read : 3293 total number of charged atoms : 3152 net assigned charge : 12.24003 assigned positive charge : 489.9337 centred at (gu) : 89.67908 90.13727 92.20020 assigned negative charge : -477.6953 centred at (gu) : 89.28013 90.26569 92.70493 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30966 grid for indexing accessible points = 1.400000 m= 26191 mr = 54860 m= 3214 mr = 18385 m= 135 mr = 1731 m= 0 mr = 37 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2177 time to turn everything in is 0.4100000 number of dielectric boundary points 35788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 268 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 24342 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) : 0.5720621 object centre at (A) : 12.17350 46.93750 56.49150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3879591E-02 7.9828277E-03 midg,1,midg; midg,igrid,midg 3.5566673E-02 1.6698733E-02 1,midg,midg; igrid,midg,midg -7.0057116E-03 1.6050898E-02 gauss-seidel spectral radius is 0.9984103 estimated iterations to convergence 199 setup time was (sec) 0.6800000 now iterating at: 12:07:17 rms-change max change #iterations 3.902000 160.1451 at 10iterations 1.710396 63.02286 at 20iterations 0.7500709 23.13409 at 30iterations 0.3305421 10.69921 at 40iterations 0.1460290 4.394659 at 50iterations 6.4202599E-02 2.136463 at 60iterations 2.8354118E-02 0.9694190 at 70iterations 1.2506438E-02 0.3974533 at 80iterations 5.5066338E-03 0.1753502 at 90iterations 2.4189616E-03 7.9351425E-02 at 100iterations 1.0724409E-03 3.7906647E-02 at 110iterations 4.7179023E-04 1.5197754E-02 at 120iterations finished qdiffx linear iterations at : 12:07:26 total time elapsed so far: 9.090000 # loops : 120 mean,max change (kT/e) : 4.7179023E-04 1.5197754E-02 energy calculations done at 9.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.220000 DelPhi exited at 12:07:26 9.225u 0.306s 0:09.83 96.8% 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 Sat Oct 15 2011 at 12:07:26 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3293 !!! WARNING: HIR 83 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.574280 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): -15.88100 40.22800 ymin,ymax (A): 16.91800 76.95700 zmin,zma (A): 25.37600 87.60700 x,y,z range (A): 56.10900 60.03900 62.23100 scale (grids/A): 2.574280 object centre (A): 12.17350 46.93750 56.49150 number of atom coordinates read : 3293 total number of charged atoms : 3152 net assigned charge : 12.24003 assigned positive charge : 489.9337 centred at (gu) : 89.51854 90.20573 93.29996 assigned negative charge : -477.6953 centred at (gu) : 88.92021 90.39852 94.05737 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 188486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30966 grid for indexing accessible points = 1.400000 m= 88945 mr = 134350 m= 27335 mr = 70639 m= 5240 mr = 20927 m= 544 mr = 3615 m= 15 mr = 308 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 7274 time to turn everything in is 1.050000 number of dielectric boundary points 80726 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 25173 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) : 1.716186 object centre at (A) : 12.17350 46.93750 56.49150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6870080 8.6265735E-02 midg,1,midg; midg,igrid,midg 0.5920969 0.3696289 1,midg,midg; igrid,midg,midg -4.3241072E-02 0.2268759 gauss-seidel spectral radius is 0.9992211 estimated iterations to convergence 283 setup time was (sec) 1.360000 now iterating at: 12:07:28 rms-change max change #iterations 9.887391 330.9959 at 10iterations 5.749172 142.7097 at 20iterations 3.319042 78.31683 at 30iterations 1.903845 39.56159 at 40iterations 1.090132 22.44122 at 50iterations 0.6208892 12.75705 at 60iterations 0.3532961 6.732624 at 70iterations 0.2008883 3.973288 at 80iterations 0.1142477 2.110798 at 90iterations 6.4834997E-02 1.311375 at 100iterations 3.6660310E-02 0.6643615 at 110iterations 2.0809688E-02 0.4327235 at 120iterations 1.1747264E-02 0.2084513 at 130iterations 6.6620070E-03 0.1306343 at 140iterations 3.7750928E-03 7.2649956E-02 at 150iterations 2.1395118E-03 4.1587830E-02 at 160iterations 1.2079440E-03 2.2254944E-02 at 170iterations 6.8444066E-04 1.1924744E-02 at 180iterations finished qdiffx linear iterations at : 12:07:42 total time elapsed so far: 15.25000 # loops : 180 mean,max change (kT/e) : 6.8444066E-04 1.1924744E-02 energy calculations done at 15.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.37000 DelPhi exited at 12:07:42 15.376u 0.353s 0:16.07 97.8% 0+0k 0+0io 0pf+0w