Sun Oct 9 19:55:41 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 Sun Oct 9 2011 at 19:55:41 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5505 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5044136 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): 3.237000 67.98900 ymin,ymax (A): -8.816000 53.26900 zmin,zma (A): -2.231000 68.34600 x,y,z range (A): 64.75200 62.08500 70.57700 scale (grids/A): 0.5044136 object centre (A): 35.61300 22.22650 33.05750 number of atom coordinates read : 5505 total number of charged atoms : 5336 net assigned charge : 5.740034 assigned positive charge : 842.8028 centred at (gu) : 88.09188 89.31734 88.76624 assigned negative charge : -837.0689 centred at (gu) : 88.00923 89.35833 88.66868 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8846 nv = 96 ne = 84 npr = 112861 no. pairs analyzed = 112861 no. exposed pairs = 6311 no. arc points = 42833 no. surface atoms = 2159 nbur = 3346 mkacc time = 0.2000000 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 = 1.708000 m= 307 mr = 4938 m= 0 mr = 5 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4210 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4219 ## 594 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 11882 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2570251E-10 2.0885448E-10 midg,1,midg; midg,igrid,midg 1.9427533E-10 -2.2286752E-11 1,midg,midg; igrid,midg,midg -2.1326148E-10 1.5474810E-10 gauss-seidel spectral radius is 0.9799431 estimated iterations to convergence 58 setup time was (sec) 0.5600000 now iterating at: 19:55:41 rms-change max change #iterations 7.3951505E-02 10.38369 at 10iterations 1.0006546E-02 1.633240 at 20iterations 4.0991451E-03 0.7424469 at 30iterations 1.8824375E-03 0.3385239 at 40iterations 8.7866909E-04 0.1541824 at 50iterations finished qdiffx linear iterations at : 19:55:44 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 8.7866909E-04 0.1541824 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 19:55:45 3.615u 0.186s 0:04.09 92.6% 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 19:55:45 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5505 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.513241 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): 3.237000 67.98900 ymin,ymax (A): -8.816000 53.26900 zmin,zma (A): -2.231000 68.34600 x,y,z range (A): 64.75200 62.08500 70.57700 scale (grids/A): 1.513241 object centre (A): 35.61300 22.22650 33.05750 number of atom coordinates read : 5505 total number of charged atoms : 5336 net assigned charge : 5.740034 assigned positive charge : 842.8028 centred at (gu) : 84.27416 87.95027 86.29700 assigned negative charge : -837.0689 centred at (gu) : 84.02766 88.07458 86.00575 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 101278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42833 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 30720 mr = 73200 m= 2729 mr = 21279 m= 50 mr = 1181 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 267 time to turn everything in is 0.4900000 number of dielectric boundary points 39117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 557 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 39827 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) : 0.5044136 object centre at (A) : 35.61300 22.22650 33.05750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4478090E-02 1.9576054E-02 midg,1,midg; midg,igrid,midg 1.2567149E-02 4.3266467E-03 1,midg,midg; igrid,midg,midg -7.6742442E-03 5.5482453E-03 gauss-seidel spectral radius is 0.9981050 estimated iterations to convergence 183 setup time was (sec) 0.7100000 now iterating at: 19:55:46 rms-change max change #iterations 4.077111 166.3355 at 10iterations 1.671594 52.09795 at 20iterations 0.6850405 20.34299 at 30iterations 0.2808796 9.989424 at 40iterations 0.1165666 3.584157 at 50iterations 4.9353331E-02 1.451332 at 60iterations 2.1977425E-02 0.7559700 at 70iterations 1.1033263E-02 0.3738909 at 80iterations 6.5601999E-03 0.2277613 at 90iterations 4.4034598E-03 0.1480980 at 100iterations 3.1688169E-03 0.1096344 at 110iterations 2.3351337E-03 7.4897766E-02 at 120iterations finished qdiffx linear iterations at : 19:55:53 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 2.3351337E-03 7.4897766E-02 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 19:55:53 8.101u 0.204s 0:08.58 96.7% 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 Sun Oct 9 2011 at 19:55:54 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5505 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.269861 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): 3.237000 67.98900 ymin,ymax (A): -8.816000 53.26900 zmin,zma (A): -2.231000 68.34600 x,y,z range (A): 64.75200 62.08500 70.57700 scale (grids/A): 2.269861 object centre (A): 35.61300 22.22650 33.05750 number of atom coordinates read : 5505 total number of charged atoms : 5336 net assigned charge : 5.740034 assigned positive charge : 842.8028 centred at (gu) : 81.41096 86.92509 84.44516 assigned negative charge : -837.0689 centred at (gu) : 81.04148 87.11182 84.00852 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 236365 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42833 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 110225 mr = 179064 m= 28721 mr = 88520 m= 3859 mr = 21195 m= 199 mr = 2348 m= 2 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 822 time to turn everything in is 1.190000 number of dielectric boundary points 88148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 42522 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) : 1.513241 object centre at (A) : 35.61300 22.22650 33.05750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3365902 0.6388920 midg,1,midg; midg,igrid,midg 0.2195538 5.0619438E-02 1,midg,midg; igrid,midg,midg -0.2430020 8.0275245E-02 gauss-seidel spectral radius is 0.9991603 estimated iterations to convergence 273 setup time was (sec) 1.440000 now iterating at: 19:55:55 rms-change max change #iterations 10.86762 251.0900 at 10iterations 6.179158 121.0820 at 20iterations 3.491546 67.28168 at 30iterations 1.961842 37.30566 at 40iterations 1.098083 18.97880 at 50iterations 0.6132703 12.35145 at 60iterations 0.3435315 6.750719 at 70iterations 0.1916798 3.224876 at 80iterations 0.1070774 2.025620 at 90iterations 6.0039524E-02 1.199146 at 100iterations 3.3883575E-02 0.5969853 at 110iterations 1.9527160E-02 0.3762283 at 120iterations 1.1654221E-02 0.2393379 at 130iterations 7.3188874E-03 0.1611938 at 140iterations 4.9460987E-03 0.1015778 at 150iterations 3.5947009E-03 7.2456360E-02 at 160iterations 2.7664248E-03 5.3161621E-02 at 170iterations 2.2017132E-03 4.3266296E-02 at 180iterations finished qdiffx linear iterations at : 19:56:07 total time elapsed so far: 13.09000 # loops : 180 mean,max change (kT/e) : 2.2017132E-03 4.3266296E-02 energy calculations done at 13.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 19:56:07 13.226u 0.204s 0:13.74 97.6% 0+0k 0+0io 0pf+0w