Sun Oct 9 22:26:37 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 22:26:37 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3190 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: 0.5739899 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): -26.20300 35.62800 ymin,ymax (A): 5.609000 67.63100 zmin,zma (A): -0.6540000 52.88200 x,y,z range (A): 61.83100 62.02200 53.53600 scale (grids/A): 0.5739899 object centre (A): 4.712500 36.62000 26.11400 number of atom coordinates read : 3190 total number of charged atoms : 3042 net assigned charge : 4.500012 assigned positive charge : 485.3586 centred at (gu) : 92.35841 89.54411 89.15614 assigned negative charge : -480.8600 centred at (gu) : 92.42468 89.61370 89.11653 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6939 nv = 96 ne = 84 npr = 62820 no. pairs analyzed = 62820 no. exposed pairs = 4296 no. arc points = 30892 no. surface atoms = 1432 nbur = 1758 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= 291 mr = 3412 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3200000 number of dielectric boundary points 3806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3103 ## 387 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8889 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9838877E-11 1.3027631E-09 midg,1,midg; midg,igrid,midg 2.4044122E-09 -4.7133264E-10 1,midg,midg; igrid,midg,midg 1.2098567E-09 -8.6700680E-10 gauss-seidel spectral radius is 0.9843612 estimated iterations to convergence 66 setup time was (sec) 0.5400000 now iterating at: 22:26:37 rms-change max change #iterations 9.8571867E-02 15.64790 at 10iterations 7.5959009E-03 1.134911 at 20iterations 5.7052594E-04 8.0093384E-02 at 30iterations 4.9633687E-05 6.7863464E-03 at 40iterations 7.1717654E-06 8.9097023E-04 at 50iterations finished qdiffx linear iterations at : 22:26:40 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 7.1717654E-06 8.9097023E-04 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 22:26:40 3.121u 0.155s 0:03.55 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 22:26:40 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3190 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: 1.721970 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): -26.20300 35.62800 ymin,ymax (A): 5.609000 67.63100 zmin,zma (A): -0.6540000 52.88200 x,y,z range (A): 61.83100 62.02200 53.53600 scale (grids/A): 1.721970 object centre (A): 4.712500 36.62000 26.11400 number of atom coordinates read : 3190 total number of charged atoms : 3042 net assigned charge : 4.500012 assigned positive charge : 485.3586 centred at (gu) : 97.07441 88.63132 87.46763 assigned negative charge : -480.8600 centred at (gu) : 97.27352 88.84079 87.34940 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30892 grid for indexing accessible points = 1.400000 m= 23111 mr = 49215 m= 2726 mr = 15479 m= 98 mr = 1386 m= 3 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 83 time to turn everything in is 0.5300000 number of dielectric boundary points 35230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 307 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 23505 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) : 0.5739899 object centre at (A) : 4.712500 36.62000 26.11400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0266734E-03 1.0861455E-02 midg,1,midg; midg,igrid,midg 2.7789113E-03 3.8092132E-03 1,midg,midg; igrid,midg,midg -4.2717615E-03 5.8664656E-03 gauss-seidel spectral radius is 0.9984056 estimated iterations to convergence 199 setup time was (sec) 0.7800000 now iterating at: 22:26:41 rms-change max change #iterations 3.906378 222.0371 at 10iterations 1.714797 62.48473 at 20iterations 0.7525017 25.44891 at 30iterations 0.3303089 12.17228 at 40iterations 0.1449413 5.254557 at 50iterations 6.3530385E-02 2.059436 at 60iterations 2.8118031E-02 1.107831 at 70iterations 1.2314631E-02 0.4592075 at 80iterations 5.4230825E-03 0.1995416 at 90iterations 2.3864082E-03 8.4403992E-02 at 100iterations 1.0512260E-03 3.8116932E-02 at 110iterations 4.6319710E-04 1.5781403E-02 at 120iterations finished qdiffx linear iterations at : 22:26:47 total time elapsed so far: 6.760000 # loops : 120 mean,max change (kT/e) : 4.6319710E-04 1.5781403E-02 energy calculations done at 6.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 22:26:48 6.968u 0.162s 0:07.47 95.3% 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 22:26:48 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3190 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: 2.582955 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): -26.20300 35.62800 ymin,ymax (A): 5.609000 67.63100 zmin,zma (A): -0.6540000 52.88200 x,y,z range (A): 61.83100 62.02200 53.53600 scale (grids/A): 2.582955 object centre (A): 4.712500 36.62000 26.11400 number of atom coordinates read : 3190 total number of charged atoms : 3042 net assigned charge : 4.500012 assigned positive charge : 485.3586 centred at (gu) : 100.6115 87.94673 86.20116 assigned negative charge : -480.8600 centred at (gu) : 100.9103 88.26099 86.02385 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 174890 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30892 grid for indexing accessible points = 1.400000 m= 78623 mr = 121027 m= 23478 mr = 60708 m= 4440 mr = 17466 m= 456 mr = 3022 m= 17 mr = 226 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 288 time to turn everything in is 1.250000 number of dielectric boundary points 79452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 24325 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) : 1.721970 object centre at (A) : 4.712500 36.62000 26.11400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1589766 0.1618404 midg,1,midg; midg,igrid,midg 5.4271214E-02 -3.9954265E-03 1,midg,midg; igrid,midg,midg -9.1695495E-02 0.2336076 gauss-seidel spectral radius is 0.9992185 estimated iterations to convergence 282 setup time was (sec) 1.540000 now iterating at: 22:26:49 rms-change max change #iterations 9.872311 335.3203 at 10iterations 5.750638 166.4508 at 20iterations 3.319871 80.74448 at 30iterations 1.908924 41.26985 at 40iterations 1.097278 25.24127 at 50iterations 0.6275097 12.94814 at 60iterations 0.3585052 7.504522 at 70iterations 0.2047215 4.996967 at 80iterations 0.1162895 2.272624 at 90iterations 6.6195950E-02 1.336983 at 100iterations 3.7578296E-02 0.7450027 at 110iterations 2.1316005E-02 0.4072313 at 120iterations 1.2094264E-02 0.2331052 at 130iterations 6.8619833E-03 0.1226645 at 140iterations 3.8939801E-03 7.4820518E-02 at 150iterations 2.1997425E-03 4.0878296E-02 at 160iterations 1.2466453E-03 2.4870403E-02 at 170iterations 7.0697261E-04 1.3221741E-02 at 180iterations finished qdiffx linear iterations at : 22:26:59 total time elapsed so far: 10.92000 # loops : 180 mean,max change (kT/e) : 7.0697261E-04 1.3221741E-02 energy calculations done at 10.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.08000 DelPhi exited at 22:26:59 11.087u 0.168s 0:11.56 97.2% 0+0k 0+0io 0pf+0w