Mon Oct 10 10:27:29 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 10:27:29 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3373 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: 0.5829185 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): -83.05200 -21.98000 ymin,ymax (A): -82.48800 -31.84800 zmin,zma (A): -13.91000 46.90900 x,y,z range (A): 61.07200 50.64000 60.81900 scale (grids/A): 0.5829185 object centre (A): -52.51600 -57.16800 16.49950 number of atom coordinates read : 3373 total number of charged atoms : 3217 net assigned charge : 9.000030 assigned positive charge : 501.3880 centred at (gu) : 87.48432 89.96594 90.65430 assigned negative charge : -492.3891 centred at (gu) : 87.49824 89.95438 90.71329 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8089 nv = 96 ne = 84 npr = 62289 no. pairs analyzed = 62289 no. exposed pairs = 5271 no. arc points = 37773 no. surface atoms = 1747 nbur = 1626 mkacc time = 0.1600000 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= 452 mr = 3667 m= 0 mr = 29 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 4845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3586 ## 360 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9758 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2017344E-09 6.5581507E-10 midg,1,midg; midg,igrid,midg 1.8658868E-09 2.4488818E-09 1,midg,midg; igrid,midg,midg 4.5217026E-09 1.0287439E-09 gauss-seidel spectral radius is 0.9848686 estimated iterations to convergence 67 setup time was (sec) 0.6700000 now iterating at: 10:27:30 rms-change max change #iterations 0.1061253 17.00608 at 10iterations 8.4875487E-03 1.262840 at 20iterations 6.9977646E-04 0.1006565 at 30iterations 8.2657200E-05 9.6054077E-03 at 40iterations 1.8105864E-05 1.6746521E-03 at 50iterations finished qdiffx linear iterations at : 10:27:34 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 1.8105864E-05 1.6746521E-03 energy calculations done at 4.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 10:27:35 4.557u 0.375s 0:05.21 94.4% 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 10:27:35 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3373 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: 1.748755 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): -83.05200 -21.98000 ymin,ymax (A): -82.48800 -31.84800 zmin,zma (A): -13.91000 46.90900 x,y,z range (A): 61.07200 50.64000 60.81900 scale (grids/A): 1.748755 object centre (A): -52.51600 -57.16800 16.49950 number of atom coordinates read : 3373 total number of charged atoms : 3217 net assigned charge : 9.000030 assigned positive charge : 501.3880 centred at (gu) : 82.45210 89.89701 91.96197 assigned negative charge : -492.3891 centred at (gu) : 82.49430 89.86257 92.13952 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 85402 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37773 grid for indexing accessible points = 1.400000 m= 29027 mr = 52954 m= 4116 mr = 19019 m= 202 mr = 2088 m= 0 mr = 44 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 44642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 319 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 25037 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) : 0.5829185 object centre at (A) : -52.51600 -57.16800 16.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1876882E-04 5.3790474E-04 midg,1,midg; midg,igrid,midg 3.3887026E-03 1.4922964E-02 1,midg,midg; igrid,midg,midg -3.2453582E-02 3.5493178E-03 gauss-seidel spectral radius is 0.9985036 estimated iterations to convergence 205 setup time was (sec) 1.080000 now iterating at: 10:27:36 rms-change max change #iterations 4.121809 191.6301 at 10iterations 1.852711 61.31183 at 20iterations 0.8328224 28.56678 at 30iterations 0.3742560 11.71848 at 40iterations 0.1685461 5.887674 at 50iterations 7.6116040E-02 2.333164 at 60iterations 3.4260612E-02 1.110446 at 70iterations 1.5466894E-02 0.4963284 at 80iterations 6.9745774E-03 0.2392039 at 90iterations 3.1551502E-03 9.3360901E-02 at 100iterations 1.4250812E-03 4.5917392E-02 at 110iterations 6.4424006E-04 1.9683838E-02 at 120iterations finished qdiffx linear iterations at : 10:27:47 total time elapsed so far: 11.75000 # loops : 120 mean,max change (kT/e) : 6.4424006E-04 1.9683838E-02 energy calculations done at 11.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 10:27:47 11.938u 0.421s 0:12.66 97.5% 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 Mon Oct 10 2011 at 10:27:47 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3373 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: 2.623133 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): -83.05200 -21.98000 ymin,ymax (A): -82.48800 -31.84800 zmin,zma (A): -13.91000 46.90900 x,y,z range (A): 61.07200 50.64000 60.81900 scale (grids/A): 2.623133 object centre (A): -52.51600 -57.16800 16.49950 number of atom coordinates read : 3373 total number of charged atoms : 3217 net assigned charge : 9.000030 assigned positive charge : 501.3880 centred at (gu) : 78.67799 89.84543 92.94289 assigned negative charge : -492.3891 centred at (gu) : 78.74132 89.79375 93.20909 start vw surface at 0.1400000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 196823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37773 grid for indexing accessible points = 1.400000 m= 93311 mr = 130315 m= 32255 mr = 70535 m= 6856 mr = 23600 m= 794 mr = 4506 m= 44 mr = 460 m= 0 mr = 2 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.830000 number of dielectric boundary points 100665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 25726 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) : 1.748755 object centre at (A) : -52.51600 -57.16800 16.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2208816 -4.4163447E-02 midg,1,midg; midg,igrid,midg -1.7633310E-03 0.1456528 1,midg,midg; igrid,midg,midg -0.3868804 0.1187491 gauss-seidel spectral radius is 0.9992757 estimated iterations to convergence 293 setup time was (sec) 2.190000 now iterating at: 10:27:50 rms-change max change #iterations 10.64098 298.9926 at 10iterations 6.482213 183.9075 at 20iterations 3.883561 84.23689 at 30iterations 2.311906 50.24984 at 40iterations 1.366032 27.62626 at 50iterations 0.8035005 16.07262 at 60iterations 0.4689701 9.339370 at 70iterations 0.2746356 5.252076 at 80iterations 0.1601428 3.259649 at 90iterations 9.3182892E-02 1.826177 at 100iterations 5.4194894E-02 1.093386 at 110iterations 3.1422731E-02 0.5808439 at 120iterations 1.8222943E-02 0.3574562 at 130iterations 1.0576101E-02 0.1860046 at 140iterations 6.1245523E-03 0.1079636 at 150iterations 3.5394877E-03 7.0038080E-02 at 160iterations 2.0499364E-03 3.4851074E-02 at 170iterations 1.1887160E-03 2.1381378E-02 at 180iterations finished qdiffx linear iterations at : 10:28:07 total time elapsed so far: 19.02000 # loops : 180 mean,max change (kT/e) : 1.1887160E-03 2.1381378E-02 energy calculations done at 19.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.19000 DelPhi exited at 10:28:07 19.191u 0.464s 0:19.97 98.3% 0+0k 0+0io 0pf+0w