Mon Oct 10 17:02:58 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 17:02:58 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2379 !!! WARNING: HIR 119 has a net charge of 0.5140 !!! WARNING: HIR 123 has a net charge of 0.5140 !!! WARNING: HIR 129 has a net charge of 0.5140 !!! WARNING: GLU 168 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: 0.5870616 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): 17.51500 75.66800 ymin,ymax (A): 5.320000 65.96100 zmin,zma (A): -14.99500 25.17400 x,y,z range (A): 58.15300 60.64100 40.16900 scale (grids/A): 0.5870616 object centre (A): 46.59150 35.64050 5.089500 number of atom coordinates read : 2379 total number of charged atoms : 2247 net assigned charge : -4.957984 assigned positive charge : 346.8443 centred at (gu) : 89.18542 90.48866 90.35235 assigned negative charge : -351.8027 centred at (gu) : 89.13288 90.48649 90.33862 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5533 nv = 96 ne = 84 npr = 48114 no. pairs analyzed = 48114 no. exposed pairs = 3194 no. arc points = 23245 no. surface atoms = 1067 nbur = 1312 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 = 1.484000 m= 248 mr = 2726 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.3700000 number of dielectric boundary points 3042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2367 ## 259 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 6951 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5449991E-09 -1.1567692E-09 midg,1,midg; midg,igrid,midg -1.2717571E-09 -1.4765290E-09 1,midg,midg; igrid,midg,midg -3.0543217E-09 -1.9677833E-10 gauss-seidel spectral radius is 0.9849805 estimated iterations to convergence 67 setup time was (sec) 0.6700000 now iterating at: 17:02:59 rms-change max change #iterations 9.9946514E-02 18.70245 at 10iterations 7.8461599E-03 1.276609 at 20iterations 6.3411117E-04 0.1110592 at 30iterations 5.1472925E-05 8.2950592E-03 at 40iterations 4.3294945E-06 7.3337555E-04 at 50iterations finished qdiffx linear iterations at : 17:03:02 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 4.3294945E-06 7.3337555E-04 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 17:03:03 4.311u 0.229s 0:05.35 84.6% 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 Mon Oct 10 2011 at 17:03:03 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2379 !!! WARNING: HIR 119 has a net charge of 0.5140 !!! WARNING: HIR 123 has a net charge of 0.5140 !!! WARNING: HIR 129 has a net charge of 0.5140 !!! WARNING: GLU 168 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: 1.761185 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): 17.51500 75.66800 ymin,ymax (A): 5.320000 65.96100 zmin,zma (A): -14.99500 25.17400 x,y,z range (A): 58.15300 60.64100 40.16900 scale (grids/A): 1.761185 object centre (A): 46.59150 35.64050 5.089500 number of atom coordinates read : 2379 total number of charged atoms : 2247 net assigned charge : -4.957984 assigned positive charge : 346.8443 centred at (gu) : 87.55579 91.46564 91.05664 assigned negative charge : -351.8027 centred at (gu) : 87.39843 91.45939 91.01562 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 60134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23245 grid for indexing accessible points = 1.400000 m= 18659 mr = 38978 m= 2188 mr = 12613 m= 81 mr = 1105 m= 0 mr = 15 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 542 time to turn everything in is 0.5800000 number of dielectric boundary points 28351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 17535 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) : 0.5870616 object centre at (A) : 46.59150 35.64050 5.089500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1394278E-03 -5.0218231E-03 midg,1,midg; midg,igrid,midg -6.3847668E-02 6.7558722E-03 1,midg,midg; igrid,midg,midg -2.9425700E-03 1.3367337E-02 gauss-seidel spectral radius is 0.9983930 estimated iterations to convergence 198 setup time was (sec) 0.9500000 now iterating at: 17:03:05 rms-change max change #iterations 3.439991 184.3310 at 10iterations 1.509519 54.79118 at 20iterations 0.6619563 23.92186 at 30iterations 0.2877473 11.31621 at 40iterations 0.1264977 4.561234 at 50iterations 5.5415601E-02 2.033909 at 60iterations 2.4251692E-02 0.8544998 at 70iterations 1.0667929E-02 0.3990479 at 80iterations 4.6553980E-03 0.1695023 at 90iterations 2.0508142E-03 8.0485344E-02 at 100iterations 8.9363690E-04 3.4772873E-02 at 110iterations 3.9395617E-04 1.4772415E-02 at 120iterations finished qdiffx linear iterations at : 17:03:13 total time elapsed so far: 9.230000 # loops : 120 mean,max change (kT/e) : 3.9395617E-04 1.4772415E-02 energy calculations done at 9.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.470000 DelPhi exited at 17:03:14 9.471u 0.239s 0:10.46 92.7% 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 Mon Oct 10 2011 at 17:03:14 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2379 !!! WARNING: HIR 119 has a net charge of 0.5140 !!! WARNING: HIR 123 has a net charge of 0.5140 !!! WARNING: HIR 129 has a net charge of 0.5140 !!! WARNING: GLU 168 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: 2.641777 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): 17.51500 75.66800 ymin,ymax (A): 5.320000 65.96100 zmin,zma (A): -14.99500 25.17400 x,y,z range (A): 58.15300 60.64100 40.16900 scale (grids/A): 2.641777 object centre (A): 46.59150 35.64050 5.089500 number of atom coordinates read : 2379 total number of charged atoms : 2247 net assigned charge : -4.957984 assigned positive charge : 346.8443 centred at (gu) : 86.33372 92.19843 91.58484 assigned negative charge : -351.8027 centred at (gu) : 86.09771 92.18902 91.52338 start vw surface at 0.1900000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 139219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23245 grid for indexing accessible points = 1.400000 m= 63634 mr = 95752 m= 18729 mr = 49388 m= 3467 mr = 13811 m= 328 mr = 2339 m= 9 mr = 153 m= 0 mr = 4 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 1868 time to turn everything in is 1.380000 number of dielectric boundary points 63939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 17971 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) : 1.761185 object centre at (A) : 46.59150 35.64050 5.089500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1031817 -5.4692898E-02 midg,1,midg; midg,igrid,midg -1.249507 -4.4741981E-02 1,midg,midg; igrid,midg,midg -0.1035812 0.2240399 gauss-seidel spectral radius is 0.9991982 estimated iterations to convergence 279 setup time was (sec) 1.780000 now iterating at: 17:03:16 rms-change max change #iterations 8.579449 308.1741 at 10iterations 4.957593 164.1484 at 20iterations 2.831148 69.34209 at 30iterations 1.607166 41.76513 at 40iterations 0.9119220 20.84413 at 50iterations 0.5154369 11.17569 at 60iterations 0.2910957 6.076881 at 70iterations 0.1643057 3.493037 at 80iterations 9.2374638E-02 2.152657 at 90iterations 5.1859602E-02 1.133698 at 100iterations 2.9159287E-02 0.6084614 at 110iterations 1.6418010E-02 0.3257999 at 120iterations 9.2250705E-03 0.1897125 at 130iterations 5.1678456E-03 0.1246796 at 140iterations 2.9038000E-03 6.4270020E-02 at 150iterations 1.6294807E-03 3.9123535E-02 at 160iterations 9.1243500E-04 1.8712997E-02 at 170iterations 5.1255053E-04 1.1285782E-02 at 180iterations finished qdiffx linear iterations at : 17:03:29 total time elapsed so far: 14.78000 # loops : 180 mean,max change (kT/e) : 5.1255053E-04 1.1285782E-02 energy calculations done at 14.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.02000 DelPhi exited at 17:03:30 15.021u 0.252s 0:16.41 93.0% 0+0k 0+0io 0pf+0w