Mon Oct 10 19:34:25 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 19:34:25 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3041 !!! WARNING: HIR 117 has a net charge of 0.5140 !!! WARNING: HIR 243 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6016257 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): -11.37800 45.51700 ymin,ymax (A): -17.91000 39.72200 zmin,zma (A): -12.86600 46.30700 x,y,z range (A): 56.89500 57.63200 59.17300 scale (grids/A): 0.6016257 object centre (A): 17.06950 10.90600 16.72050 number of atom coordinates read : 3041 total number of charged atoms : 2900 net assigned charge : -1.471975 assigned positive charge : 461.0200 centred at (gu) : 88.77856 89.35126 90.50745 assigned negative charge : -462.4934 centred at (gu) : 88.78806 89.32246 90.53626 start vw surface at 0.1400000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7288 nv = 96 ne = 84 npr = 60891 no. pairs analyzed = 60891 no. exposed pairs = 4216 no. arc points = 29675 no. surface atoms = 1409 nbur = 1632 mkacc time = 0.1700000 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 = 1.456000 m= 369 mr = 3544 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 4084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2928 ## 272 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 9077 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8205701E-10 -2.2131843E-09 midg,1,midg; midg,igrid,midg -2.2852871E-09 5.6239863E-10 1,midg,midg; igrid,midg,midg -2.7923566E-10 -8.2827495E-10 gauss-seidel spectral radius is 0.9857472 estimated iterations to convergence 69 setup time was (sec) 0.8700000 now iterating at: 19:34:27 rms-change max change #iterations 0.1193506 24.69663 at 10iterations 1.0257659E-02 1.546094 at 20iterations 1.0869247E-03 0.2104168 at 30iterations 2.4257539E-04 4.7798157E-02 at 40iterations 8.1817969E-05 1.5909195E-02 at 50iterations finished qdiffx linear iterations at : 19:34:33 total time elapsed so far: 7.180000 # loops : 50 mean,max change (kT/e) : 8.1817969E-05 1.5909195E-02 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 19:34:34 7.353u 0.761s 0:08.52 95.1% 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 19:34:34 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3041 !!! WARNING: HIR 117 has a net charge of 0.5140 !!! WARNING: HIR 243 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.804877 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): -11.37800 45.51700 ymin,ymax (A): -17.91000 39.72200 zmin,zma (A): -12.86600 46.30700 x,y,z range (A): 56.89500 57.63200 59.17300 scale (grids/A): 1.804877 object centre (A): 17.06950 10.90600 16.72050 number of atom coordinates read : 3041 total number of charged atoms : 2900 net assigned charge : -1.471975 assigned positive charge : 461.0200 centred at (gu) : 86.33495 88.05253 91.52136 assigned negative charge : -462.4934 centred at (gu) : 86.36389 87.96707 91.60857 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 78508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29675 grid for indexing accessible points = 1.400000 m= 26241 mr = 50920 m= 3781 mr = 17815 m= 148 mr = 2080 m= 0 mr = 16 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.8100000 number of dielectric boundary points 37847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 22636 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) : 0.6016257 object centre at (A) : 17.06950 10.90600 16.72050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9445353E-03 -2.3366442E-02 midg,1,midg; midg,igrid,midg 7.9389010E-03 1.6638489E-02 1,midg,midg; igrid,midg,midg 5.3984597E-03 -2.5820853E-03 gauss-seidel spectral radius is 0.9985430 estimated iterations to convergence 208 setup time was (sec) 1.370000 now iterating at: 19:34:36 rms-change max change #iterations 4.294501 172.7265 at 10iterations 1.947049 72.91092 at 20iterations 0.8857695 32.83611 at 30iterations 0.4051378 12.61808 at 40iterations 0.1842915 6.127771 at 50iterations 8.4104523E-02 2.617310 at 60iterations 3.8374256E-02 1.296990 at 70iterations 1.7546969E-02 0.5283737 at 80iterations 8.0370326E-03 0.2607970 at 90iterations 3.7062021E-03 0.1258912 at 100iterations 1.7470684E-03 5.5484772E-02 at 110iterations 8.4659655E-04 3.0214310E-02 at 120iterations finished qdiffx linear iterations at : 19:34:54 total time elapsed so far: 18.94000 # loops : 120 mean,max change (kT/e) : 8.4659655E-04 3.0214310E-02 energy calculations done at 18.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.11000 DelPhi exited at 19:34:55 19.113u 0.909s 0:20.60 97.1% 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 19:34:55 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3041 !!! WARNING: HIR 117 has a net charge of 0.5140 !!! WARNING: HIR 243 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.707316 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): -11.37800 45.51700 ymin,ymax (A): -17.91000 39.72200 zmin,zma (A): -12.86600 46.30700 x,y,z range (A): 56.89500 57.63200 59.17300 scale (grids/A): 2.707316 object centre (A): 17.06950 10.90600 16.72050 number of atom coordinates read : 3041 total number of charged atoms : 2900 net assigned charge : -1.471975 assigned positive charge : 461.0200 centred at (gu) : 84.50233 87.07880 92.28191 assigned negative charge : -462.4934 centred at (gu) : 84.54576 86.95055 92.41286 start vw surface at 0.1500000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 181759 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29675 grid for indexing accessible points = 1.400000 m= 85242 mr = 125249 m= 29327 mr = 66122 m= 6473 mr = 21969 m= 688 mr = 4406 m= 19 mr = 351 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 60 time to turn everything in is 2.090000 number of dielectric boundary points 85408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.350000 number of grid points assigned charge 23192 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) : 1.804877 object centre at (A) : 17.06950 10.90600 16.72050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2932707E-02 -0.2800847 midg,1,midg; midg,igrid,midg 0.1438304 0.3189957 1,midg,midg; igrid,midg,midg 0.1340765 -5.1939230E-02 gauss-seidel spectral radius is 0.9992549 estimated iterations to convergence 289 setup time was (sec) 2.720000 now iterating at: 19:34:58 rms-change max change #iterations 10.40258 341.5714 at 10iterations 6.152242 139.7569 at 20iterations 3.598600 79.44595 at 30iterations 2.091770 43.48864 at 40iterations 1.215910 26.60040 at 50iterations 0.7050632 13.94944 at 60iterations 0.4067184 7.786513 at 70iterations 0.2345510 4.462256 at 80iterations 0.1354347 2.628294 at 90iterations 7.7947505E-02 1.528654 at 100iterations 4.4954594E-02 0.8236637 at 110iterations 2.5901154E-02 0.4654541 at 120iterations 1.4895214E-02 0.2661018 at 130iterations 8.6265700E-03 0.1624413 at 140iterations 5.0007640E-03 9.7496033E-02 at 150iterations 2.9305005E-03 5.3338051E-02 at 160iterations 1.7502073E-03 3.3615112E-02 at 170iterations 1.0800187E-03 2.4014473E-02 at 180iterations finished qdiffx linear iterations at : 19:35:30 total time elapsed so far: 34.68000 # loops : 180 mean,max change (kT/e) : 1.0800187E-03 2.4014473E-02 energy calculations done at 34.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 34.84000 DelPhi exited at 19:35:31 34.846u 0.905s 0:36.21 98.7% 0+0k 0+0io 0pf+0w