Sat Oct 8 14:20:23 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 8 2011 at 14:20:23 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6248025 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): -14.34800 35.32200 ymin,ymax (A): -12.13500 44.84300 zmin,zma (A): -40.01600 12.66200 x,y,z range (A): 49.67000 56.97800 52.67800 scale (grids/A): 0.6248025 object centre (A): 10.48700 16.35400 -13.67700 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : 1.4008060E-02 assigned positive charge : 456.5586 centred at (gu) : 91.77401 91.83852 91.13415 assigned negative charge : -456.5453 centred at (gu) : 91.82478 91.75722 91.19948 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7771 nv = 96 ne = 84 npr = 63635 no. pairs analyzed = 63635 no. exposed pairs = 3486 no. arc points = 24379 no. surface atoms = 1195 nbur = 1838 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 353 mr = 4474 m= 3 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2300000 number of dielectric boundary points 3610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2368 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9589 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5165449E-09 -7.5123801E-09 midg,1,midg; midg,igrid,midg -4.8440434E-09 1.0902481E-08 1,midg,midg; igrid,midg,midg 3.0613523E-09 -6.7296351E-09 gauss-seidel spectral radius is 0.9867635 estimated iterations to convergence 71 setup time was (sec) 0.4100000 now iterating at: 14:20:24 rms-change max change #iterations 0.1464554 20.40851 at 10iterations 1.4144052E-02 1.766329 at 20iterations 1.4582331E-03 0.2292519 at 30iterations 1.9020701E-04 2.5238037E-02 at 40iterations 3.3420638E-05 4.7340393E-03 at 50iterations finished qdiffx linear iterations at : 14:20:27 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 3.3420638E-05 4.7340393E-03 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.720000 DelPhi exited at 14:20:27 3.719u 0.169s 0:04.18 92.5% 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 Sat Oct 8 2011 at 14:20:27 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.874408 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): -14.34800 35.32200 ymin,ymax (A): -12.13500 44.84300 zmin,zma (A): -40.01600 12.66200 x,y,z range (A): 49.67000 56.97800 52.67800 scale (grids/A): 1.874408 object centre (A): 10.48700 16.35400 -13.67700 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : 1.4008060E-02 assigned positive charge : 456.5586 centred at (gu) : 95.32156 95.51492 93.40211 assigned negative charge : -456.5453 centred at (gu) : 95.47423 95.27127 93.59797 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85122 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24379 grid for indexing accessible points = 1.400000 m= 30034 mr = 61226 m= 4144 mr = 22401 m= 196 mr = 2461 m= 3 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 33358 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 22649 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) : 0.6248025 object centre at (A) : 10.48700 16.35400 -13.67700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3585030E-02 9.3089631E-03 midg,1,midg; midg,igrid,midg -1.4684354E-02 4.8249699E-02 1,midg,midg; igrid,midg,midg 7.2000381E-03 -1.2900288E-02 gauss-seidel spectral radius is 0.9986261 estimated iterations to convergence 214 setup time was (sec) 0.6200000 now iterating at: 14:20:28 rms-change max change #iterations 4.560111 164.4837 at 10iterations 2.129088 63.26480 at 20iterations 0.9953781 30.67330 at 30iterations 0.4658895 13.53167 at 40iterations 0.2183662 5.869243 at 50iterations 0.1026197 3.022396 at 60iterations 4.8064824E-02 1.543526 at 70iterations 2.2500692E-02 0.6911783 at 80iterations 1.0547004E-02 0.3052473 at 90iterations 4.9431529E-03 0.1466856 at 100iterations 2.3224915E-03 6.8995476E-02 at 110iterations 1.0884890E-03 3.2783508E-02 at 120iterations finished qdiffx linear iterations at : 14:20:35 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 1.0884890E-03 3.2783508E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 14:20:36 7.811u 0.200s 0:08.32 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 Sat Oct 8 2011 at 14:20:36 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.811611 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): -14.34800 35.32200 ymin,ymax (A): -12.13500 44.84300 zmin,zma (A): -40.01600 12.66200 x,y,z range (A): 49.67000 56.97800 52.67800 scale (grids/A): 2.811611 object centre (A): 10.48700 16.35400 -13.67700 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : 1.4008060E-02 assigned positive charge : 456.5586 centred at (gu) : 97.98221 98.27232 95.10293 assigned negative charge : -456.5453 centred at (gu) : 98.21125 97.90686 95.39700 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 197568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24379 grid for indexing accessible points = 1.400000 m= 99531 mr = 148426 m= 33764 mr = 82480 m= 7214 mr = 27059 m= 881 mr = 5275 m= 42 mr = 522 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 75231 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 23083 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) : 1.874408 object centre at (A) : 10.48700 16.35400 -13.67700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1307543 0.2404917 midg,1,midg; midg,igrid,midg -9.9356152E-02 0.6933758 1,midg,midg; igrid,midg,midg 0.1155048 -0.1091732 gauss-seidel spectral radius is 0.9992605 estimated iterations to convergence 290 setup time was (sec) 1.310000 now iterating at: 14:20:37 rms-change max change #iterations 10.62640 289.9116 at 10iterations 6.217802 128.6567 at 20iterations 3.620118 69.36791 at 30iterations 2.097117 38.51272 at 40iterations 1.215666 20.45469 at 50iterations 0.7012365 13.13189 at 60iterations 0.4061903 6.879604 at 70iterations 0.2341520 4.083337 at 80iterations 0.1349858 2.417751 at 90iterations 7.7762648E-02 1.347099 at 100iterations 4.4679709E-02 0.8107483 at 110iterations 2.5787599E-02 0.4613118 at 120iterations 1.4837055E-02 0.2621460 at 130iterations 8.5502826E-03 0.1440263 at 140iterations 4.9226950E-03 8.0732346E-02 at 150iterations 2.8390433E-03 4.8376083E-02 at 160iterations 1.6377143E-03 2.7153015E-02 at 170iterations 9.4435114E-04 1.5579224E-02 at 180iterations finished qdiffx linear iterations at : 14:20:49 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 9.4435114E-04 1.5579224E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 14:20:49 12.919u 0.216s 0:13.46 97.4% 0+0k 0+0io 0pf+0w