Tue Oct 11 07:38:42 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 07:38:42 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 = 2644 !!! WARNING: SEP 202 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6990672 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): -12.92800 37.99700 ymin,ymax (A): -22.11800 25.43400 zmin,zma (A): -6.562000 40.03100 x,y,z range (A): 50.92500 47.55200 46.59300 scale (grids/A): 0.6990672 object centre (A): 12.53450 1.658000 16.73450 number of atom coordinates read : 2644 total number of charged atoms : 2288 net assigned charge : 5.025004 assigned positive charge : 364.1762 centred at (gu) : 91.03635 88.56616 89.74455 assigned negative charge : -359.1518 centred at (gu) : 91.10580 88.54335 89.87672 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8066 nv = 96 ne = 84 npr = 49486 no. pairs analyzed = 49486 no. exposed pairs = 2866 no. arc points = 19723 no. surface atoms = 977 nbur = 1667 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 509 mr = 4765 m= 3 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1818 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9028 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0127098E-07 -2.6378324E-08 midg,1,midg; midg,igrid,midg 3.1734338E-08 3.4756180E-08 1,midg,midg; igrid,midg,midg 5.5114274E-08 2.1587363E-09 gauss-seidel spectral radius is 0.9893680 estimated iterations to convergence 79 setup time was (sec) 0.5300000 now iterating at: 07:38:42 rms-change max change #iterations 0.2099969 30.80056 at 10iterations 2.6228173E-02 3.645927 at 20iterations 3.6662226E-03 0.4612274 at 30iterations 6.5931911E-04 0.1001205 at 40iterations 1.5414583E-04 2.2712708E-02 at 50iterations finished qdiffx linear iterations at : 07:38:45 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.5414583E-04 2.2712708E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 07:38:46 3.399u 0.225s 0:03.99 90.4% 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 07:38:46 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 = 2644 !!! WARNING: SEP 202 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.097202 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): -12.92800 37.99700 ymin,ymax (A): -22.11800 25.43400 zmin,zma (A): -6.562000 40.03100 x,y,z range (A): 50.92500 47.55200 46.59300 scale (grids/A): 2.097202 object centre (A): 12.53450 1.658000 16.73450 number of atom coordinates read : 2644 total number of charged atoms : 2288 net assigned charge : 5.025004 assigned positive charge : 364.1762 centred at (gu) : 93.10863 85.69800 89.23320 assigned negative charge : -359.1518 centred at (gu) : 93.31725 85.62993 89.62999 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 85141 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19723 grid for indexing accessible points = 1.400000 m= 34518 mr = 60988 m= 6732 mr = 26819 m= 549 mr = 4605 m= 12 mr = 287 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 34253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 18162 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) : 0.6990672 object centre at (A) : 12.53450 1.658000 16.73450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7213318E-02 -1.3109537E-02 midg,1,midg; midg,igrid,midg 1.5261071E-02 2.2739735E-02 1,midg,midg; igrid,midg,midg 1.7558780E-02 1.8093076E-02 gauss-seidel spectral radius is 0.9988363 estimated iterations to convergence 232 setup time was (sec) 0.9900000 now iterating at: 07:38:47 rms-change max change #iterations 4.903985 230.5379 at 10iterations 2.436703 80.68613 at 20iterations 1.211064 32.73388 at 30iterations 0.6036388 17.47667 at 40iterations 0.3007472 9.016888 at 50iterations 0.1500191 4.228313 at 60iterations 7.4745446E-02 2.071312 at 70iterations 3.7347179E-02 1.060087 at 80iterations 1.8777970E-02 0.5274887 at 90iterations 9.4809141E-03 0.2791862 at 100iterations 4.8341453E-03 0.1455879 at 110iterations 2.4970800E-03 7.3478699E-02 at 120iterations finished qdiffx linear iterations at : 07:38:54 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 2.4970800E-03 7.3478699E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 07:38:54 7.921u 0.259s 0:08.49 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 Tue Oct 11 2011 at 07:38:54 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 = 2644 !!! WARNING: SEP 202 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.145802 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): -12.92800 37.99700 ymin,ymax (A): -22.11800 25.43400 zmin,zma (A): -6.562000 40.03100 x,y,z range (A): 50.92500 47.55200 46.59300 scale (grids/A): 3.145802 object centre (A): 12.53450 1.658000 16.73450 number of atom coordinates read : 2644 total number of charged atoms : 2288 net assigned charge : 5.025004 assigned positive charge : 364.1762 centred at (gu) : 94.66277 83.54689 88.84968 assigned negative charge : -359.1518 centred at (gu) : 94.97588 83.44483 89.44492 start vw surface at 0.1700000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 196418 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19723 grid for indexing accessible points = 1.400000 m= 107178 mr = 146715 m= 44264 mr = 90397 m= 12817 mr = 37054 m= 2373 mr = 10103 m= 237 mr = 1770 m= 8 mr = 157 m= 0 mr = 2 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.960000 number of dielectric boundary points 77097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 18302 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) : 2.097202 object centre at (A) : 12.53450 1.658000 16.73450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2120661E-02 -0.1555077 midg,1,midg; midg,igrid,midg 0.1107803 0.1208825 1,midg,midg; igrid,midg,midg 1.0150594E-02 2.0952836E-02 gauss-seidel spectral radius is 0.9992983 estimated iterations to convergence 298 setup time was (sec) 2.290000 now iterating at: 07:38:57 rms-change max change #iterations 10.82679 421.6065 at 10iterations 6.358164 135.4519 at 20iterations 3.740459 74.17361 at 30iterations 2.196439 36.45731 at 40iterations 1.289236 26.07055 at 50iterations 0.7531426 12.31157 at 60iterations 0.4402638 8.371448 at 70iterations 0.2581882 4.443468 at 80iterations 0.1507668 2.489060 at 90iterations 8.8350795E-02 1.390888 at 100iterations 5.1937088E-02 0.8463440 at 110iterations 3.0549325E-02 0.4957390 at 120iterations 1.8163946E-02 0.3324814 at 130iterations 1.0961758E-02 0.1888428 at 140iterations 6.7773950E-03 0.1185532 at 150iterations 4.3497351E-03 7.9750061E-02 at 160iterations 2.9306139E-03 5.0727844E-02 at 170iterations 2.0817018E-03 3.7879944E-02 at 180iterations finished qdiffx linear iterations at : 07:39:08 total time elapsed so far: 13.21000 # loops : 180 mean,max change (kT/e) : 2.0817018E-03 3.7879944E-02 energy calculations done at 13.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.42000 DelPhi exited at 07:39:08 13.424u 0.244s 0:14.09 96.9% 0+0k 0+0io 0pf+0w