Sun Oct 9 08:20:27 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 Sun Oct 9 2011 at 08:20:27 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6164 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.4658771 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): 3.876000 80.29100 ymin,ymax (A): 22.57500 85.43600 zmin,zma (A): 6.638999 70.69500 x,y,z range (A): 76.41500 62.86100 64.05600 scale (grids/A): 0.4658771 object centre (A): 42.08350 54.00550 38.66700 number of atom coordinates read : 6164 total number of charged atoms : 5996 net assigned charge : -1.985986 assigned positive charge : 932.6754 centred at (gu) : 89.88750 88.79902 89.26752 assigned negative charge : -934.6697 centred at (gu) : 89.82547 88.79106 89.13976 start vw surface at 0.2700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 8108 nv = 96 ne = 84 npr = 124650 no. pairs analyzed = 124650 no. exposed pairs = 7746 no. arc points = 53117 no. surface atoms = 2588 nbur = 3576 mkacc time = 0.3500000 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 = 1.820000 m= 221 mr = 4035 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 4293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4869 ## 918 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 11155 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0443359E-11 4.0144495E-11 midg,1,midg; midg,igrid,midg -8.3849429E-12 4.5870160E-13 1,midg,midg; igrid,midg,midg -2.9661586E-11 2.2256747E-11 gauss-seidel spectral radius is 0.9765567 estimated iterations to convergence 54 setup time was (sec) 0.9500000 now iterating at: 08:20:28 rms-change max change #iterations 4.7493875E-02 12.25699 at 10iterations 2.2854130E-03 0.4617462 at 20iterations 3.0233792E-04 7.9813004E-02 at 30iterations 7.8918347E-05 2.1301270E-02 at 40iterations 2.2946107E-05 6.0138702E-03 at 50iterations finished qdiffx linear iterations at : 08:20:32 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 2.2946107E-05 6.0138702E-03 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 08:20:32 4.446u 0.259s 0:04.99 93.9% 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 Sun Oct 9 2011 at 08:20:32 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6164 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.397631 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): 3.876000 80.29100 ymin,ymax (A): 22.57500 85.43600 zmin,zma (A): 6.638999 70.69500 x,y,z range (A): 76.41500 62.86100 64.05600 scale (grids/A): 1.397631 object centre (A): 42.08350 54.00550 38.66700 number of atom coordinates read : 6164 total number of charged atoms : 5996 net assigned charge : -1.985986 assigned positive charge : 932.6754 centred at (gu) : 89.66091 86.39539 87.80009 assigned negative charge : -934.6697 centred at (gu) : 89.47632 86.37300 87.41897 start vw surface at 0.2500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 94058 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53117 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 23699 mr = 63769 m= 1464 mr = 14668 m= 18 mr = 461 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 789 time to turn everything in is 0.8600000 number of dielectric boundary points 40341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 952 ## 22 charges are in solution ## iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 43370 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) : 0.4658771 object centre at (A) : 42.08350 54.00550 38.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8856568E-03 4.5595709E-03 midg,1,midg; midg,igrid,midg -1.3461933E-03 -1.0486516E-03 1,midg,midg; igrid,midg,midg -6.6379230E-03 -7.2355312E-03 gauss-seidel spectral radius is 0.9978035 estimated iterations to convergence 170 setup time was (sec) 1.160000 now iterating at: 08:20:33 rms-change max change #iterations 3.539885 136.5409 at 10iterations 1.354008 50.94344 at 20iterations 0.5193576 17.45271 at 30iterations 0.1984425 6.560005 at 40iterations 7.6042607E-02 2.960629 at 50iterations 2.9145349E-02 1.030987 at 60iterations 1.1204957E-02 0.3484802 at 70iterations 4.3124487E-03 0.1440985 at 80iterations 1.6544861E-03 5.1818848E-02 at 90iterations 6.4076623E-04 2.1683693E-02 at 100iterations 2.4952937E-04 8.2883835E-03 at 110iterations 9.8978337E-05 3.3512115E-03 at 120iterations finished qdiffx linear iterations at : 08:20:42 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 9.8978337E-05 3.3512115E-03 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 08:20:42 9.657u 0.305s 0:10.30 96.6% 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 Sun Oct 9 2011 at 08:20:42 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6164 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 2.096447 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): 3.876000 80.29100 ymin,ymax (A): 22.57500 85.43600 zmin,zma (A): 6.638999 70.69500 x,y,z range (A): 76.41500 62.86100 64.05600 scale (grids/A): 2.096447 object centre (A): 42.08350 54.00550 38.66700 number of atom coordinates read : 6164 total number of charged atoms : 5996 net assigned charge : -1.985986 assigned positive charge : 932.6754 centred at (gu) : 89.49113 84.59238 86.69964 assigned negative charge : -934.6697 centred at (gu) : 89.21437 84.55933 86.12843 start vw surface at 0.2600000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 220158 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53117 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 90649 mr = 158177 m= 18132 mr = 68367 m= 1613 mr = 12059 m= 42 mr = 802 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 2716 time to turn everything in is 2.050000 number of dielectric boundary points 91189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 47594 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) : 1.397631 object centre at (A) : 42.08350 54.00550 38.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1065766 5.0664850E-02 midg,1,midg; midg,igrid,midg -1.0585224E-02 -7.7502835E-03 1,midg,midg; igrid,midg,midg -1.4891710E-02 -0.5999463 gauss-seidel spectral radius is 0.9991007 estimated iterations to convergence 263 setup time was (sec) 2.390000 now iterating at: 08:20:45 rms-change max change #iterations 10.33520 310.5613 at 10iterations 5.847618 129.8694 at 20iterations 3.290308 79.58878 at 30iterations 1.839412 41.86291 at 40iterations 1.022774 21.80297 at 50iterations 0.5670151 11.47599 at 60iterations 0.3135202 6.136183 at 70iterations 0.1729543 3.549180 at 80iterations 9.5034674E-02 1.962531 at 90iterations 5.2163724E-02 0.9689941 at 100iterations 2.8667711E-02 0.5257635 at 110iterations 1.5733166E-02 0.2972800 at 120iterations 8.6103277E-03 0.1702728 at 130iterations 4.7152280E-03 9.6267700E-02 at 140iterations 2.5739546E-03 5.1729679E-02 at 150iterations 1.4099869E-03 2.6416779E-02 at 160iterations 7.7277439E-04 1.4743805E-02 at 170iterations 4.2396662E-04 8.3160400E-03 at 180iterations finished qdiffx linear iterations at : 08:20:59 total time elapsed so far: 16.33000 # loops : 180 mean,max change (kT/e) : 4.2396662E-04 8.3160400E-03 energy calculations done at 16.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.51000 DelPhi exited at 08:20:59 16.507u 0.299s 0:17.06 98.4% 0+0k 0+0io 0pf+0w