Tue Oct 11 06:09:47 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 06:09:47 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: SEP 190 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7502951 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): 3.592000 46.41200 ymin,ymax (A): 0.6220001 40.20600 zmin,zma (A): -2.212000 45.23600 x,y,z range (A): 42.82000 39.58400 47.44800 scale (grids/A): 0.7502951 object centre (A): 25.00200 20.41400 21.51200 number of atom coordinates read : 1994 total number of charged atoms : 1864 net assigned charge : 6.025005 assigned positive charge : 303.0902 centred at (gu) : 90.34254 90.49737 90.57494 assigned negative charge : -297.0652 centred at (gu) : 90.53669 90.45670 90.65388 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7810 nv = 96 ne = 84 npr = 39879 no. pairs analyzed = 39879 no. exposed pairs = 2421 no. arc points = 16745 no. surface atoms = 834 nbur = 1160 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 592 mr = 4553 m= 2 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3703 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1338 ## 119 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 8080 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0231003E-07 4.5371383E-08 midg,1,midg; midg,igrid,midg 7.9403776E-08 1.9784854E-07 1,midg,midg; igrid,midg,midg 3.3304053E-07 -1.0253695E-07 gauss-seidel spectral radius is 0.9907260 estimated iterations to convergence 84 setup time was (sec) 0.3400000 now iterating at: 06:09:48 rms-change max change #iterations 0.2586870 34.92333 at 10iterations 3.6528401E-02 4.671883 at 20iterations 5.2190018E-03 0.6866980 at 30iterations 8.5147348E-04 0.1282654 at 40iterations 1.8777013E-04 2.5165558E-02 at 50iterations finished qdiffx linear iterations at : 06:09:50 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.8777013E-04 2.5165558E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 06:09:51 3.302u 0.180s 0:03.77 92.3% 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 06:09:51 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: SEP 190 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.250885 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): 3.592000 46.41200 ymin,ymax (A): 0.6220001 40.20600 zmin,zma (A): -2.212000 45.23600 x,y,z range (A): 42.82000 39.58400 47.44800 scale (grids/A): 2.250885 object centre (A): 25.00200 20.41400 21.51200 number of atom coordinates read : 1994 total number of charged atoms : 1864 net assigned charge : 6.025005 assigned positive charge : 303.0902 centred at (gu) : 91.02766 91.49228 91.72508 assigned negative charge : -297.0652 centred at (gu) : 91.61021 91.37035 91.96179 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 82040 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16745 grid for indexing accessible points = 1.400000 m= 34685 mr = 58607 m= 7621 mr = 26765 m= 822 mr = 5291 m= 22 mr = 456 m= 0 mr = 6 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 34065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 48 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 14851 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) : 0.7502951 object centre at (A) : 25.00200 20.41400 21.51200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9541403E-02 2.4049230E-02 midg,1,midg; midg,igrid,midg 6.4132009E-03 4.3359090E-02 1,midg,midg; igrid,midg,midg 5.9208248E-02 6.2989858E-03 gauss-seidel spectral radius is 0.9989368 estimated iterations to convergence 243 setup time was (sec) 0.6400000 now iterating at: 06:09:52 rms-change max change #iterations 5.065711 204.5352 at 10iterations 2.601382 82.09362 at 20iterations 1.336983 40.43893 at 30iterations 0.6884006 20.98244 at 40iterations 0.3549565 11.86287 at 50iterations 0.1816056 4.990906 at 60iterations 9.3571812E-02 2.641999 at 70iterations 4.8074782E-02 1.290947 at 80iterations 2.4814785E-02 0.6708565 at 90iterations 1.2914210E-02 0.3937340 at 100iterations 6.7496938E-03 0.1834545 at 110iterations 3.5473104E-03 0.1010818 at 120iterations finished qdiffx linear iterations at : 06:09:59 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 3.5473104E-03 0.1010818 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 06:09:59 7.771u 0.182s 0:08.38 94.8% 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 06:09:59 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: SEP 190 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.376328 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): 3.592000 46.41200 ymin,ymax (A): 0.6220001 40.20600 zmin,zma (A): -2.212000 45.23600 x,y,z range (A): 42.82000 39.58400 47.44800 scale (grids/A): 3.376328 object centre (A): 25.00200 20.41400 21.51200 number of atom coordinates read : 1994 total number of charged atoms : 1864 net assigned charge : 6.025005 assigned positive charge : 303.0902 centred at (gu) : 91.54148 92.23863 92.58758 assigned negative charge : -297.0652 centred at (gu) : 92.41537 92.05550 92.94274 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 188755 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16745 grid for indexing accessible points = 1.400000 m= 106039 mr = 140552 m= 46280 mr = 89018 m= 14615 mr = 38661 m= 3289 mr = 11617 m= 447 mr = 2498 m= 20 mr = 320 m= 0 mr = 5 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 76774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 14912 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) : 2.250885 object centre at (A) : 25.00200 20.41400 21.51200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3976247 0.3211935 midg,1,midg; midg,igrid,midg -6.8573686E-03 0.3044688 1,midg,midg; igrid,midg,midg 0.3964623 0.1766435 gauss-seidel spectral radius is 0.9993212 estimated iterations to convergence 303 setup time was (sec) 1.500000 now iterating at: 06:10:01 rms-change max change #iterations 10.90333 290.6785 at 10iterations 6.505200 129.2590 at 20iterations 3.887145 73.54195 at 30iterations 2.311067 45.24857 at 40iterations 1.372867 23.41212 at 50iterations 0.8135698 15.61676 at 60iterations 0.4820014 8.234679 at 70iterations 0.2861282 5.057255 at 80iterations 0.1692526 2.640373 at 90iterations 0.1001098 1.714580 at 100iterations 5.9390124E-02 0.9901317 at 110iterations 3.5415329E-02 0.5960963 at 120iterations 2.1260962E-02 0.3506222 at 130iterations 1.2968611E-02 0.2057571 at 140iterations 8.1447642E-03 0.1469193 at 150iterations 5.3330241E-03 8.6467743E-02 at 160iterations 3.6783996E-03 6.5628052E-02 at 170iterations 2.7043591E-03 4.9186707E-02 at 180iterations finished qdiffx linear iterations at : 06:10:12 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 2.7043591E-03 4.9186707E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 06:10:13 12.879u 0.218s 0:13.86 94.3% 0+0k 0+0io 0pf+0w