Tue Oct 11 07:53:19 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 07:53:19 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: THS 97 has a net charge of 0.4660 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.6421241 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): -1.446000 53.99500 ymin,ymax (A): -22.72600 23.04600 zmin,zma (A): 9.080999 54.32200 x,y,z range (A): 55.44100 45.77200 45.24100 scale (grids/A): 0.6421241 object centre (A): 26.27450 0.1599998 31.70150 number of atom coordinates read : 2380 total number of charged atoms : 2232 net assigned charge : 6.425008 assigned positive charge : 360.7343 centred at (gu) : 88.69074 90.29254 90.12862 assigned negative charge : -354.3098 centred at (gu) : 88.67136 90.20387 89.91447 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6636 nv = 96 ne = 84 npr = 47952 no. pairs analyzed = 47952 no. exposed pairs = 2885 no. arc points = 20259 no. surface atoms = 974 nbur = 1406 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 3719 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1988 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4349989E-08 3.4428226E-08 midg,1,midg; midg,igrid,midg -1.2155306E-10 2.1084064E-08 1,midg,midg; igrid,midg,midg 1.0102694E-08 9.2359773E-09 gauss-seidel spectral radius is 0.9874145 estimated iterations to convergence 73 setup time was (sec) 0.5000000 now iterating at: 07:53:20 rms-change max change #iterations 0.1436218 22.94146 at 10iterations 1.4626902E-02 2.144217 at 20iterations 1.6988062E-03 0.2590179 at 30iterations 2.5463279E-04 3.6823273E-02 at 40iterations 5.0511990E-05 7.4462891E-03 at 50iterations finished qdiffx linear iterations at : 07:53:22 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 5.0511990E-05 7.4462891E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 07:53:23 3.120u 0.157s 0:03.66 89.3% 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 07:53:23 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: THS 97 has a net charge of 0.4660 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 1.926372 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): -1.446000 53.99500 ymin,ymax (A): -22.72600 23.04600 zmin,zma (A): 9.080999 54.32200 x,y,z range (A): 55.44100 45.77200 45.24100 scale (grids/A): 1.926372 object centre (A): 26.27450 0.1599998 31.70150 number of atom coordinates read : 2380 total number of charged atoms : 2232 net assigned charge : 6.425008 assigned positive charge : 360.7343 centred at (gu) : 86.07193 90.87727 90.38553 assigned negative charge : -354.3098 centred at (gu) : 86.01403 90.61150 89.74326 start vw surface at 0.1900000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 71704 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20259 grid for indexing accessible points = 1.400000 m= 27157 mr = 50332 m= 4207 mr = 20355 m= 243 mr = 2562 m= 3 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 29971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 17579 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) : 0.6421241 object centre at (A) : 26.27450 0.1599998 31.70150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1268753E-02 4.4456143E-02 midg,1,midg; midg,igrid,midg -2.2184404E-03 1.1360856E-02 1,midg,midg; igrid,midg,midg 1.6244492E-02 2.9345000E-02 gauss-seidel spectral radius is 0.9986438 estimated iterations to convergence 215 setup time was (sec) 0.8100000 now iterating at: 07:53:24 rms-change max change #iterations 4.134550 209.6129 at 10iterations 1.932279 76.77666 at 20iterations 0.9153500 31.22440 at 30iterations 0.4305609 13.34769 at 40iterations 0.2033063 6.541616 at 50iterations 9.5116459E-02 3.121643 at 60iterations 4.4837169E-02 1.761330 at 70iterations 2.1180158E-02 0.6793137 at 80iterations 9.9989157E-03 0.3371081 at 90iterations 4.7313231E-03 0.1599121 at 100iterations 2.2561329E-03 8.0085039E-02 at 110iterations 1.0832014E-03 3.6346436E-02 at 120iterations finished qdiffx linear iterations at : 07:53:30 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 1.0832014E-03 3.6346436E-02 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 07:53:30 6.964u 0.168s 0:07.41 96.0% 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 07:53:30 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: THS 97 has a net charge of 0.4660 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.889558 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): -1.446000 53.99500 ymin,ymax (A): -22.72600 23.04600 zmin,zma (A): 9.080999 54.32200 x,y,z range (A): 55.44100 45.77200 45.24100 scale (grids/A): 2.889558 object centre (A): 26.27450 0.1599998 31.70150 number of atom coordinates read : 2380 total number of charged atoms : 2232 net assigned charge : 6.425008 assigned positive charge : 360.7343 centred at (gu) : 84.10782 91.31591 90.57831 assigned negative charge : -354.3098 centred at (gu) : 84.02103 90.91729 89.61481 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 165373 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20259 grid for indexing accessible points = 1.400000 m= 86887 mr = 121176 m= 32129 mr = 71954 m= 7461 mr = 26057 m= 996 mr = 5441 m= 63 mr = 703 m= 0 mr = 30 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.370000 number of dielectric boundary points 67548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 17852 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) : 1.926372 object centre at (A) : 26.27450 0.1599998 31.70150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2937480 0.4520233 midg,1,midg; midg,igrid,midg -3.7703294E-02 2.5012927E-02 1,midg,midg; igrid,midg,midg 4.4934887E-02 0.2031804 gauss-seidel spectral radius is 0.9992535 estimated iterations to convergence 289 setup time was (sec) 1.650000 now iterating at: 07:53:32 rms-change max change #iterations 9.667916 402.7668 at 10iterations 5.640407 135.3156 at 20iterations 3.272560 66.45164 at 30iterations 1.896149 36.50953 at 40iterations 1.097738 22.42124 at 50iterations 0.6338720 12.80230 at 60iterations 0.3647993 7.200085 at 70iterations 0.2099123 3.836235 at 80iterations 0.1206224 2.454144 at 90iterations 6.9436401E-02 1.297819 at 100iterations 3.9881431E-02 0.7171049 at 110iterations 2.2914244E-02 0.4716187 at 120iterations 1.3212243E-02 0.2397614 at 130iterations 7.5887279E-03 0.1535664 at 140iterations 4.4031455E-03 8.2942963E-02 at 150iterations 2.5638836E-03 4.7286987E-02 at 160iterations 1.5100660E-03 2.7465820E-02 at 170iterations 9.1026170E-04 1.7400742E-02 at 180iterations finished qdiffx linear iterations at : 07:53:43 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 9.1026170E-04 1.7400742E-02 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 07:53:43 12.255u 0.186s 0:12.88 96.5% 0+0k 0+0io 0pf+0w