Tue Oct 11 07:34:35 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 07:34:35 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3242 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5919127 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): 0.2390000 48.44000 ymin,ymax (A): -8.131000 49.27300 zmin,zma (A): 0.8609999 61.00500 x,y,z range (A): 48.20100 57.40400 60.14400 scale (grids/A): 0.5919127 object centre (A): 24.33950 20.57100 30.93300 number of atom coordinates read : 3242 total number of charged atoms : 3092 net assigned charge : -1.999987 assigned positive charge : 490.4898 centred at (gu) : 89.87853 89.30669 90.82032 assigned negative charge : -492.4909 centred at (gu) : 89.79395 89.22493 90.78088 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7454 nv = 96 ne = 84 npr = 66530 no. pairs analyzed = 66530 no. exposed pairs = 3892 no. arc points = 26366 no. surface atoms = 1322 nbur = 1920 mkacc time = 0.1400000 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 = 1.456000 m= 389 mr = 4284 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3600000 number of dielectric boundary points 3524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2723 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9455 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7075972E-09 9.4169206E-10 midg,1,midg; midg,igrid,midg -4.2337001E-09 1.9249973E-09 1,midg,midg; igrid,midg,midg -3.8109484E-09 2.2997990E-09 gauss-seidel spectral radius is 0.9852796 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 07:34:36 rms-change max change #iterations 0.1149213 14.66889 at 10iterations 1.0464205E-02 1.663666 at 20iterations 1.5100302E-03 0.2445431 at 30iterations 4.5252062E-04 8.2784653E-02 at 40iterations 1.5606146E-04 2.8791428E-02 at 50iterations finished qdiffx linear iterations at : 07:34:39 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.5606146E-04 2.8791428E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 07:34:39 3.489u 0.198s 0:04.18 87.7% 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 07:34:39 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3242 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: 1.775738 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): 0.2390000 48.44000 ymin,ymax (A): -8.131000 49.27300 zmin,zma (A): 0.8609999 61.00500 x,y,z range (A): 48.20100 57.40400 60.14400 scale (grids/A): 1.775738 object centre (A): 24.33950 20.57100 30.93300 number of atom coordinates read : 3242 total number of charged atoms : 3092 net assigned charge : -1.999987 assigned positive charge : 490.4898 centred at (gu) : 89.63486 87.91921 92.45985 assigned negative charge : -492.4909 centred at (gu) : 89.38139 87.67448 92.34240 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26366 grid for indexing accessible points = 1.400000 m= 29301 mr = 57581 m= 4169 mr = 21813 m= 178 mr = 2633 m= 0 mr = 44 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1796 time to turn everything in is 0.5700000 number of dielectric boundary points 32638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 24090 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) : 0.5919127 object centre at (A) : 24.33950 20.57100 30.93300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1093853E-03 2.9746168E-03 midg,1,midg; midg,igrid,midg -1.8143304E-02 6.2222737E-03 1,midg,midg; igrid,midg,midg -1.6718520E-02 2.8688307E-03 gauss-seidel spectral radius is 0.9984944 estimated iterations to convergence 204 setup time was (sec) 0.8600000 now iterating at: 07:34:40 rms-change max change #iterations 4.245275 209.5942 at 10iterations 1.919066 72.08644 at 20iterations 0.8687956 27.29483 at 30iterations 0.3911492 12.05711 at 40iterations 0.1766125 5.637779 at 50iterations 8.0083743E-02 2.436289 at 60iterations 3.6352918E-02 1.106604 at 70iterations 1.6466260E-02 0.6031590 at 80iterations 7.5262967E-03 0.2344723 at 90iterations 3.4754321E-03 0.1202850 at 100iterations 1.6597509E-03 5.2503586E-02 at 110iterations 8.1967830E-04 2.7297974E-02 at 120iterations finished qdiffx linear iterations at : 07:34:47 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 8.1967830E-04 2.7297974E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 07:34:48 7.876u 0.256s 0:08.52 95.3% 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 07:34:48 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3242 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: 2.663607 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): 0.2390000 48.44000 ymin,ymax (A): -8.131000 49.27300 zmin,zma (A): 0.8609999 61.00500 x,y,z range (A): 48.20100 57.40400 60.14400 scale (grids/A): 2.663607 object centre (A): 24.33950 20.57100 30.93300 number of atom coordinates read : 3242 total number of charged atoms : 3092 net assigned charge : -1.999987 assigned positive charge : 490.4898 centred at (gu) : 89.45217 86.87846 93.68945 assigned negative charge : -492.4909 centred at (gu) : 89.07201 86.51164 93.51350 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 187816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26366 grid for indexing accessible points = 1.400000 m= 96005 mr = 139661 m= 33303 mr = 79054 m= 7334 mr = 27019 m= 880 mr = 5530 m= 22 mr = 585 m= 0 mr = 6 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 5955 time to turn everything in is 1.410000 number of dielectric boundary points 73505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 24730 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) : 1.775738 object centre at (A) : 24.33950 20.57100 30.93300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2415229 -8.1246775E-03 midg,1,midg; midg,igrid,midg -0.3421463 6.3299850E-02 1,midg,midg; igrid,midg,midg -0.2139924 2.1705611E-02 gauss-seidel spectral radius is 0.9992296 estimated iterations to convergence 284 setup time was (sec) 1.740000 now iterating at: 07:34:50 rms-change max change #iterations 10.31075 262.4429 at 10iterations 5.968179 139.7804 at 20iterations 3.443799 62.29170 at 30iterations 1.975098 40.97380 at 40iterations 1.132059 25.90285 at 50iterations 0.6468204 14.53899 at 60iterations 0.3692180 7.729412 at 70iterations 0.2113358 4.115902 at 80iterations 0.1202968 2.196245 at 90iterations 6.8614319E-02 1.198586 at 100iterations 3.8967904E-02 0.6724834 at 110iterations 2.2218384E-02 0.4136963 at 120iterations 1.2668121E-02 0.2204781 at 130iterations 7.2425324E-03 0.1295033 at 140iterations 4.1496134E-03 7.3631287E-02 at 150iterations 2.4009156E-03 4.3893814E-02 at 160iterations 1.4102316E-03 2.9363632E-02 at 170iterations 8.4448728E-04 1.5171051E-02 at 180iterations finished qdiffx linear iterations at : 07:35:01 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 8.4448728E-04 1.5171051E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 07:35:01 12.870u 0.273s 0:13.43 97.8% 0+0k 0+0io 0pf+0w