Mon Oct 10 22:22:40 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 Mon Oct 10 2011 at 22:22:41 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5881964 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): 14.41700 74.94100 ymin,ymax (A): -11.92200 43.76700 zmin,zma (A): -7.993000 35.21200 x,y,z range (A): 60.52400 55.68900 43.20500 scale (grids/A): 0.5881964 object centre (A): 44.67900 15.92250 13.60950 number of atom coordinates read : 2637 total number of charged atoms : 2491 net assigned charge : 3.406017 assigned positive charge : 395.7988 centred at (gu) : 89.28799 90.18960 89.82530 assigned negative charge : -392.3934 centred at (gu) : 89.52493 90.35375 90.01708 start vw surface at 0.2100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 5922 nv = 96 ne = 84 npr = 54000 no. pairs analyzed = 54000 no. exposed pairs = 3097 no. arc points = 21450 no. surface atoms = 1052 nbur = 1585 mkacc time = 0.1500000 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= 244 mr = 3306 m= 0 mr = 12 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.4000000 number of dielectric boundary points 2848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2208 ## 266 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 7543 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9585856E-09 -3.8679069E-09 midg,1,midg; midg,igrid,midg 4.8291890E-09 -3.4535106E-09 1,midg,midg; igrid,midg,midg 8.0497085E-09 -4.4258499E-09 gauss-seidel spectral radius is 0.9850453 estimated iterations to convergence 67 setup time was (sec) 0.7000000 now iterating at: 22:22:41 rms-change max change #iterations 0.1000487 14.94218 at 10iterations 9.0404041E-03 1.484749 at 20iterations 1.0549204E-03 0.2438354 at 30iterations 2.3759744E-04 6.1466217E-02 at 40iterations 6.0340866E-05 1.6078949E-02 at 50iterations finished qdiffx linear iterations at : 22:22:45 total time elapsed so far: 4.120000 # loops : 50 mean,max change (kT/e) : 6.0340866E-05 1.6078949E-02 energy calculations done at 4.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.360000 DelPhi exited at 22:22:46 4.365u 0.246s 0:05.17 88.9% 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 Mon Oct 10 2011 at 22:22:46 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.764589 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): 14.41700 74.94100 ymin,ymax (A): -11.92200 43.76700 zmin,zma (A): -7.993000 35.21200 x,y,z range (A): 60.52400 55.68900 43.20500 scale (grids/A): 1.764589 object centre (A): 44.67900 15.92250 13.60950 number of atom coordinates read : 2637 total number of charged atoms : 2491 net assigned charge : 3.406017 assigned positive charge : 395.7988 centred at (gu) : 87.86363 90.56838 89.47530 assigned negative charge : -392.3934 centred at (gu) : 88.57460 91.06116 90.05101 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 65514 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21450 grid for indexing accessible points = 1.400000 m= 20948 mr = 46057 m= 2515 mr = 15179 m= 65 mr = 1532 m= 0 mr = 11 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1881 time to turn everything in is 0.6200000 number of dielectric boundary points 26263 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19362 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) : 0.5881964 object centre at (A) : 44.67900 15.92250 13.60950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1564925E-02 -1.4514164E-03 midg,1,midg; midg,igrid,midg 2.5867309E-02 -2.0112518E-02 1,midg,midg; igrid,midg,midg -3.8502442E-03 -5.0049122E-02 gauss-seidel spectral radius is 0.9984121 estimated iterations to convergence 199 setup time was (sec) 1.000000 now iterating at: 22:22:47 rms-change max change #iterations 3.681453 151.9091 at 10iterations 1.617635 58.72233 at 20iterations 0.7158108 27.17006 at 30iterations 0.3143629 11.52673 at 40iterations 0.1399496 4.580799 at 50iterations 6.1829809E-02 2.274477 at 60iterations 2.7328664E-02 1.047020 at 70iterations 1.2099246E-02 0.4215345 at 80iterations 5.4054009E-03 0.1968765 at 90iterations 2.4299452E-03 8.7158203E-02 at 100iterations 1.1177342E-03 4.3926239E-02 at 110iterations 5.2848255E-04 2.2629738E-02 at 120iterations finished qdiffx linear iterations at : 22:22:55 total time elapsed so far: 9.380000 # loops : 120 mean,max change (kT/e) : 5.2848255E-04 2.2629738E-02 energy calculations done at 9.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 22:22:56 9.594u 0.288s 0:10.38 95.0% 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 Mon Oct 10 2011 at 22:22:56 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.646884 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): 14.41700 74.94100 ymin,ymax (A): -11.92200 43.76700 zmin,zma (A): -7.993000 35.21200 x,y,z range (A): 60.52400 55.68900 43.20500 scale (grids/A): 2.646884 object centre (A): 44.67900 15.92250 13.60950 number of atom coordinates read : 2637 total number of charged atoms : 2491 net assigned charge : 3.406017 assigned positive charge : 395.7988 centred at (gu) : 86.79520 90.85252 89.21294 assigned negative charge : -392.3934 centred at (gu) : 87.86192 91.59165 90.07642 start vw surface at 0.1900000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 151967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21450 grid for indexing accessible points = 1.400000 m= 71843 mr = 111833 m= 21939 mr = 58527 m= 4273 mr = 17437 m= 338 mr = 3219 m= 3 mr = 182 m= 0 mr = 0 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 6528 time to turn everything in is 1.450000 number of dielectric boundary points 59165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 19923 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) : 1.764589 object centre at (A) : 44.67900 15.92250 13.60950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2416288 5.9158406E-03 midg,1,midg; midg,igrid,midg 0.3813804 -0.5812755 1,midg,midg; igrid,midg,midg -0.1206668 -0.6929944 gauss-seidel spectral radius is 0.9991911 estimated iterations to convergence 278 setup time was (sec) 1.830000 now iterating at: 22:22:58 rms-change max change #iterations 8.902474 277.7535 at 10iterations 5.032203 110.4415 at 20iterations 2.833456 61.24311 at 30iterations 1.595583 33.30308 at 40iterations 0.8962392 18.11030 at 50iterations 0.5016195 11.18087 at 60iterations 0.2812922 6.812279 at 70iterations 0.1574196 3.187485 at 80iterations 8.8292435E-02 1.763881 at 90iterations 4.9457163E-02 0.9307327 at 100iterations 2.7735393E-02 0.5294037 at 110iterations 1.5547474E-02 0.2976370 at 120iterations 8.7454906E-03 0.1777363 at 130iterations 4.9123410E-03 0.1114426 at 140iterations 2.7848622E-03 6.1511993E-02 at 150iterations 1.5888597E-03 3.9188385E-02 at 160iterations 9.2254812E-04 2.1331787E-02 at 170iterations 5.4600759E-04 1.5125275E-02 at 180iterations finished qdiffx linear iterations at : 22:23:12 total time elapsed so far: 15.03000 # loops : 180 mean,max change (kT/e) : 5.4600759E-04 1.5125275E-02 energy calculations done at 15.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.27000 DelPhi exited at 22:23:13 15.270u 0.286s 0:16.32 95.2% 0+0k 0+0io 0pf+0w