Mon Oct 10 10:34:41 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+sph.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 = amb.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 10:34:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2713 !!! WARNING: MN9 957 has a net charge of 1.4000 !!! WARNING: MN9 958 has a net charge of 1.4000 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: 0.5878953 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): -30.04400 30.51100 ymin,ymax (A): 41.12000 98.32600 zmin,zma (A): 1.071000 52.93100 x,y,z range (A): 60.55500 57.20601 51.86000 scale (grids/A): 0.5878953 object centre (A): 0.2335005 69.72300 27.00100 number of atom coordinates read : 2713 total number of charged atoms : 2562 net assigned charge : 4.300009 assigned positive charge : 412.1069 centred at (gu) : 87.38041 90.13255 87.52721 assigned negative charge : -407.8077 centred at (gu) : 87.35197 90.15023 87.41866 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6369 nv = 96 ne = 84 npr = 51318 no. pairs analyzed = 51318 no. exposed pairs = 3901 no. arc points = 27931 no. surface atoms = 1295 nbur = 1418 mkacc time = 0.1300000 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= 334 mr = 3036 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3651 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2669 ## 292 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7793 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7969289E-09 2.3136149E-09 midg,1,midg; midg,igrid,midg 1.7156611E-09 8.8432855E-10 1,midg,midg; igrid,midg,midg 1.0166522E-09 1.1335389E-09 gauss-seidel spectral radius is 0.9850516 estimated iterations to convergence 67 setup time was (sec) 0.5700000 now iterating at: 10:34:41 rms-change max change #iterations 9.9253289E-02 16.77332 at 10iterations 8.0910726E-03 1.180965 at 20iterations 6.6894304E-04 0.1199870 at 30iterations 6.3977313E-05 1.0993004E-02 at 40iterations 9.2120417E-06 1.5563965E-03 at 50iterations finished qdiffx linear iterations at : 10:34:44 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 9.2120417E-06 1.5563965E-03 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.830000 DelPhi exited at 10:34:45 3.838u 0.166s 0:04.28 93.2% 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 10:34:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2713 !!! WARNING: MN9 957 has a net charge of 1.4000 !!! WARNING: MN9 958 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.763686 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): -30.04400 30.51100 ymin,ymax (A): 41.12000 98.32600 zmin,zma (A): 1.071000 52.93100 x,y,z range (A): 60.55500 57.20601 51.86000 scale (grids/A): 1.763686 object centre (A): 0.2335005 69.72300 27.00100 number of atom coordinates read : 2713 total number of charged atoms : 2562 net assigned charge : 4.300009 assigned positive charge : 412.1069 centred at (gu) : 82.14063 90.39703 82.58116 assigned negative charge : -407.8077 centred at (gu) : 82.05590 90.45051 82.25591 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27931 grid for indexing accessible points = 1.400000 m= 22880 mr = 44375 m= 3224 mr = 15212 m= 179 mr = 1712 m= 0 mr = 46 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 33631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 238 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 19910 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) : 0.5878953 object centre at (A) : 0.2335005 69.72300 27.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2357649E-03 3.3348103E-03 midg,1,midg; midg,igrid,midg 4.2328546E-03 -2.9919625E-04 1,midg,midg; igrid,midg,midg 3.5445843E-02 1.8402029E-02 gauss-seidel spectral radius is 0.9984333 estimated iterations to convergence 200 setup time was (sec) 0.8400000 now iterating at: 10:34:46 rms-change max change #iterations 3.775357 158.9650 at 10iterations 1.664605 64.38792 at 20iterations 0.7357401 27.15066 at 30iterations 0.3259248 10.91449 at 40iterations 0.1441076 4.796574 at 50iterations 6.3809566E-02 2.446608 at 60iterations 2.8097562E-02 0.9498692 at 70iterations 1.2465816E-02 0.4556770 at 80iterations 5.5269087E-03 0.1709191 at 90iterations 2.4493132E-03 8.7852478E-02 at 100iterations 1.0921312E-03 3.5411835E-02 at 110iterations 4.8438544E-04 1.6839504E-02 at 120iterations finished qdiffx linear iterations at : 10:34:53 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 4.8438544E-04 1.6839504E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.080000 DelPhi exited at 10:34:54 8.087u 0.215s 0:08.58 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 Mon Oct 10 2011 at 10:34:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2713 !!! WARNING: MN9 957 has a net charge of 1.4000 !!! WARNING: MN9 958 has a net charge of 1.4000 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: 2.645529 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): -30.04400 30.51100 ymin,ymax (A): 41.12000 98.32600 zmin,zma (A): 1.071000 52.93100 x,y,z range (A): 60.55500 57.20601 51.86000 scale (grids/A): 2.645529 object centre (A): 0.2335005 69.72300 27.00100 number of atom coordinates read : 2713 total number of charged atoms : 2562 net assigned charge : 4.300009 assigned positive charge : 412.1069 centred at (gu) : 78.21079 90.59544 78.87176 assigned negative charge : -407.8077 centred at (gu) : 78.08373 90.67562 78.38389 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 158852 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27931 grid for indexing accessible points = 1.400000 m= 75315 mr = 108903 m= 25300 mr = 57929 m= 5474 mr = 18748 m= 669 mr = 3696 m= 34 mr = 367 m= 0 mr = 18 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 75983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 20487 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) : 1.763686 object centre at (A) : 0.2335005 69.72300 27.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1150870E-03 -4.5869429E-02 midg,1,midg; midg,igrid,midg 0.1476885 0.3097397 1,midg,midg; igrid,midg,midg 0.5006148 0.3000721 gauss-seidel spectral radius is 0.9992194 estimated iterations to convergence 283 setup time was (sec) 1.650000 now iterating at: 10:34:55 rms-change max change #iterations 9.468493 336.6782 at 10iterations 5.555226 188.6744 at 20iterations 3.216189 69.36357 at 30iterations 1.848392 43.12653 at 40iterations 1.058423 22.38840 at 50iterations 0.6061146 12.38476 at 60iterations 0.3441090 8.282367 at 70iterations 0.1959258 4.061608 at 80iterations 0.1108252 2.474525 at 90iterations 6.3060917E-02 1.229720 at 100iterations 3.5756104E-02 0.7208099 at 110iterations 2.0221088E-02 0.3783697 at 120iterations 1.1439000E-02 0.2447586 at 130iterations 6.4887209E-03 0.1323543 at 140iterations 3.6688899E-03 7.0632935E-02 at 150iterations 2.0764314E-03 4.3772221E-02 at 160iterations 1.1752156E-03 2.5788307E-02 at 170iterations 6.6484412E-04 1.2608528E-02 at 180iterations finished qdiffx linear iterations at : 10:35:07 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 6.6484412E-04 1.2608528E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 10:35:07 13.112u 0.209s 0:13.82 96.3% 0+0k 0+0io 0pf+0w