Sun Oct 9 07:58:03 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 Sun Oct 9 2011 at 07:58:03 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2215 !!! WARNING: NDP 385 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6916919 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): 4.633000 50.12200 ymin,ymax (A): -25.05200 26.41600 zmin,zma (A): -19.67700 30.20400 x,y,z range (A): 45.48900 51.46800 49.88100 scale (grids/A): 0.6916919 object centre (A): 27.37750 0.6820002 5.263500 number of atom coordinates read : 2215 total number of charged atoms : 2073 net assigned charge : -3.499990 assigned positive charge : 338.9374 centred at (gu) : 90.07141 90.98645 90.16862 assigned negative charge : -342.4377 centred at (gu) : 90.09956 91.06873 90.27132 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7293 nv = 96 ne = 84 npr = 44565 no. pairs analyzed = 44565 no. exposed pairs = 2876 no. arc points = 20610 no. surface atoms = 958 nbur = 1257 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 489 mr = 3962 m= 2 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.2700000 number of dielectric boundary points 3740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1971 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8160 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8103258E-08 -6.1025446E-08 midg,1,midg; midg,igrid,midg 8.9711660E-09 -6.2294873E-08 1,midg,midg; igrid,midg,midg -8.9660475E-09 -3.0820551E-08 gauss-seidel spectral radius is 0.9891330 estimated iterations to convergence 78 setup time was (sec) 0.5100000 now iterating at: 07:58:04 rms-change max change #iterations 0.1941814 27.61057 at 10iterations 2.2953417E-02 3.109749 at 20iterations 2.6443547E-03 0.3526459 at 30iterations 3.0945276E-04 4.2112350E-02 at 40iterations 3.6584624E-05 5.0468445E-03 at 50iterations finished qdiffx linear iterations at : 07:58:06 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 3.6584624E-05 5.0468445E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 07:58:07 3.320u 0.195s 0:03.81 92.1% 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 Sun Oct 9 2011 at 07:58:07 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2215 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 2.075076 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): 4.633000 50.12200 ymin,ymax (A): -25.05200 26.41600 zmin,zma (A): -19.67700 30.20400 x,y,z range (A): 45.48900 51.46800 49.88100 scale (grids/A): 2.075076 object centre (A): 27.37750 0.6820002 5.263500 number of atom coordinates read : 2215 total number of charged atoms : 2073 net assigned charge : -3.499990 assigned positive charge : 338.9374 centred at (gu) : 90.21402 92.95905 90.50543 assigned negative charge : -342.4377 centred at (gu) : 90.29863 93.20612 90.81375 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77123 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20610 grid for indexing accessible points = 1.400000 m= 30391 mr = 52585 m= 6046 mr = 22731 m= 588 mr = 3988 m= 12 mr = 257 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1327 time to turn everything in is 0.5600000 number of dielectric boundary points 34599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 16434 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) : 0.6916919 object centre at (A) : 27.37750 0.6820002 5.263500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2256951E-03 -3.8724910E-02 midg,1,midg; midg,igrid,midg 2.2890078E-02 -3.3024075E-03 1,midg,midg; igrid,midg,midg -4.2332192E-03 -3.1856559E-02 gauss-seidel spectral radius is 0.9988123 estimated iterations to convergence 230 setup time was (sec) 0.8600000 now iterating at: 07:58:08 rms-change max change #iterations 4.765210 192.9759 at 10iterations 2.336599 83.72721 at 20iterations 1.150428 35.86821 at 30iterations 0.5661820 17.74983 at 40iterations 0.2788814 8.856367 at 50iterations 0.1375762 4.199095 at 60iterations 6.7421272E-02 2.223030 at 70iterations 3.3239875E-02 0.9657049 at 80iterations 1.6385939E-02 0.5101231 at 90iterations 8.0341669E-03 0.2300115 at 100iterations 3.9780918E-03 0.1243033 at 110iterations 1.9611646E-03 5.3764343E-02 at 120iterations finished qdiffx linear iterations at : 07:58:14 total time elapsed so far: 7.300000 # loops : 120 mean,max change (kT/e) : 1.9611646E-03 5.3764343E-02 energy calculations done at 7.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 07:58:15 7.472u 0.220s 0:07.95 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 07:58:15 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2215 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 3.112613 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): 4.633000 50.12200 ymin,ymax (A): -25.05200 26.41600 zmin,zma (A): -19.67700 30.20400 x,y,z range (A): 45.48900 51.46800 49.88100 scale (grids/A): 3.112613 object centre (A): 27.37750 0.6820002 5.263500 number of atom coordinates read : 2215 total number of charged atoms : 2073 net assigned charge : -3.499990 assigned positive charge : 338.9374 centred at (gu) : 90.32092 94.43841 90.75816 assigned negative charge : -342.4377 centred at (gu) : 90.44788 94.80914 91.22057 start vw surface at 0.1500000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 177417 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20610 grid for indexing accessible points = 1.400000 m= 94140 mr = 126645 m= 39035 mr = 77402 m= 11552 mr = 31923 m= 2369 mr = 8924 m= 251 mr = 1627 m= 12 mr = 142 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 4651 time to turn everything in is 1.800000 number of dielectric boundary points 78110 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 16584 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) : 2.075076 object centre at (A) : 27.37750 0.6820002 5.263500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5814030E-02 -0.2533705 midg,1,midg; midg,igrid,midg 0.7912961 7.2651528E-02 1,midg,midg; igrid,midg,midg -7.4873447E-02 -0.2963727 gauss-seidel spectral radius is 0.9992968 estimated iterations to convergence 298 setup time was (sec) 2.110000 now iterating at: 07:58:17 rms-change max change #iterations 10.66686 421.4760 at 10iterations 6.280433 139.0435 at 20iterations 3.677198 67.93806 at 30iterations 2.160834 43.26974 at 40iterations 1.265575 24.94662 at 50iterations 0.7397336 12.41032 at 60iterations 0.4324027 7.774403 at 70iterations 0.2522909 4.917535 at 80iterations 0.1470122 2.692924 at 90iterations 8.5702874E-02 1.363567 at 100iterations 5.0024390E-02 0.8778572 at 110iterations 2.9182404E-02 0.4696591 at 120iterations 1.7012808E-02 0.3076134 at 130iterations 9.9210385E-03 0.1933708 at 140iterations 5.7821912E-03 0.1016045 at 150iterations 3.3792602E-03 5.7952881E-02 at 160iterations 1.9764737E-03 3.9804459E-02 at 170iterations 1.1570973E-03 2.2155762E-02 at 180iterations finished qdiffx linear iterations at : 07:58:27 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 1.1570973E-03 2.2155762E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 07:58:28 12.696u 0.204s 0:13.16 97.9% 0+0k 0+0io 0pf+0w