Tue Oct 11 08:34:18 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 Tue Oct 11 2011 at 08:34:18 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3260 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 0.5981686 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): 71.53400 122.6050 ymin,ymax (A): -15.92700 36.48800 zmin,zma (A): -28.07900 31.43600 x,y,z range (A): 51.07101 52.41500 59.51500 scale (grids/A): 0.5981686 object centre (A): 97.06950 10.28050 1.678499 number of atom coordinates read : 3260 total number of charged atoms : 3108 net assigned charge : -0.5999874 assigned positive charge : 488.2347 centred at (gu) : 89.76327 90.25215 90.77484 assigned negative charge : -488.8358 centred at (gu) : 89.87254 90.15245 90.70696 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7575 nv = 96 ne = 84 npr = 68242 no. pairs analyzed = 68242 no. exposed pairs = 3710 no. arc points = 25175 no. surface atoms = 1267 nbur = 1993 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 341 mr = 4432 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 0.4100000 number of dielectric boundary points 3448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2566 ## 273 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 9580 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7256875E-09 3.1626475E-09 midg,1,midg; midg,igrid,midg -4.4025610E-09 4.2349444E-09 1,midg,midg; igrid,midg,midg 4.6485624E-09 -4.8215085E-09 gauss-seidel spectral radius is 0.9855822 estimated iterations to convergence 68 setup time was (sec) 0.6900000 now iterating at: 08:34:19 rms-change max change #iterations 0.1211610 17.29463 at 10iterations 1.0877676E-02 1.523369 at 20iterations 1.3105945E-03 0.2009163 at 30iterations 3.4314353E-04 6.3953400E-02 at 40iterations 1.1114399E-04 2.0847321E-02 at 50iterations finished qdiffx linear iterations at : 08:34:22 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 1.1114399E-04 2.0847321E-02 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 08:34:23 4.218u 0.267s 0:05.05 88.5% 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 Tue Oct 11 2011 at 08:34:23 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3260 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 1.794506 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): 71.53400 122.6050 ymin,ymax (A): -15.92700 36.48800 zmin,zma (A): -28.07900 31.43600 x,y,z range (A): 51.07101 52.41500 59.51500 scale (grids/A): 1.794506 object centre (A): 97.06950 10.28050 1.678499 number of atom coordinates read : 3260 total number of charged atoms : 3108 net assigned charge : -0.5999874 assigned positive charge : 488.2347 centred at (gu) : 89.28872 90.75523 92.32366 assigned negative charge : -488.8358 centred at (gu) : 89.61732 90.45695 92.12048 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 83527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25175 grid for indexing accessible points = 1.400000 m= 29183 mr = 60371 m= 3845 mr = 21987 m= 161 mr = 2382 m= 0 mr = 45 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2041 time to turn everything in is 0.7300000 number of dielectric boundary points 31931 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 24213 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) : 0.5981686 object centre at (A) : 97.06950 10.28050 1.678499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2263292E-02 7.8790225E-03 midg,1,midg; midg,igrid,midg -1.9463247E-02 -1.7440638E-03 1,midg,midg; igrid,midg,midg 2.2058461E-02 -1.8134097E-02 gauss-seidel spectral radius is 0.9985250 estimated iterations to convergence 206 setup time was (sec) 1.040000 now iterating at: 08:34:24 rms-change max change #iterations 4.298247 181.2220 at 10iterations 1.957934 64.00031 at 20iterations 0.8908994 28.22016 at 30iterations 0.4064503 13.96090 at 40iterations 0.1853912 5.980365 at 50iterations 8.4673688E-02 2.575973 at 60iterations 3.8676012E-02 1.228703 at 70iterations 1.7590009E-02 0.5684929 at 80iterations 8.0286665E-03 0.2347887 at 90iterations 3.6983225E-03 0.1088142 at 100iterations 1.7210488E-03 5.6857109E-02 at 110iterations 8.1739598E-04 2.5457382E-02 at 120iterations finished qdiffx linear iterations at : 08:34:33 total time elapsed so far: 9.530000 # loops : 120 mean,max change (kT/e) : 8.1739598E-04 2.5457382E-02 energy calculations done at 9.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.710000 DelPhi exited at 08:34:34 9.715u 0.305s 0:10.65 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 Tue Oct 11 2011 at 08:34:34 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3260 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 2.691758 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): 71.53400 122.6050 ymin,ymax (A): -15.92700 36.48800 zmin,zma (A): -28.07900 31.43600 x,y,z range (A): 51.07101 52.41500 59.51500 scale (grids/A): 2.691758 object centre (A): 97.06950 10.28050 1.678499 number of atom coordinates read : 3260 total number of charged atoms : 3108 net assigned charge : -0.5999874 assigned positive charge : 488.2347 centred at (gu) : 88.93296 91.13254 93.48530 assigned negative charge : -488.8358 centred at (gu) : 89.42579 90.68526 93.18070 start vw surface at 0.1800000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 193713 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25175 grid for indexing accessible points = 1.400000 m= 97387 mr = 145857 m= 32508 mr = 81238 m= 6546 mr = 26346 m= 771 mr = 4951 m= 26 mr = 527 m= 0 mr = 10 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 6819 time to turn everything in is 1.850000 number of dielectric boundary points 72022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 24854 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) : 1.794506 object centre at (A) : 97.06950 10.28050 1.678499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4851073 -4.0027209E-02 midg,1,midg; midg,igrid,midg -0.2274879 -0.1164699 1,midg,midg; igrid,midg,midg 0.2588916 -0.2583866 gauss-seidel spectral radius is 0.9992342 estimated iterations to convergence 285 setup time was (sec) 2.180000 now iterating at: 08:34:36 rms-change max change #iterations 10.29034 375.3929 at 10iterations 5.937156 126.5796 at 20iterations 3.426429 72.40296 at 30iterations 1.957314 39.87466 at 40iterations 1.122067 20.04900 at 50iterations 0.6416037 10.92348 at 60iterations 0.3659389 7.451834 at 70iterations 0.2086615 3.807220 at 80iterations 0.1192330 2.202417 at 90iterations 6.7888625E-02 1.223080 at 100iterations 3.8710147E-02 0.7270012 at 110iterations 2.2109175E-02 0.3776083 at 120iterations 1.2610826E-02 0.2197647 at 130iterations 7.2251372E-03 0.1283903 at 140iterations 4.1715549E-03 7.1138382E-02 at 150iterations 2.4300455E-03 4.5965195E-02 at 160iterations 1.4410408E-03 2.7383804E-02 at 170iterations 8.8595913E-04 1.7930984E-02 at 180iterations finished qdiffx linear iterations at : 08:34:50 total time elapsed so far: 16.35000 # loops : 180 mean,max change (kT/e) : 8.8595913E-04 1.7930984E-02 energy calculations done at 16.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.53000 DelPhi exited at 08:34:51 16.533u 0.328s 0:17.42 96.7% 0+0k 0+0io 0pf+0w