Sat Oct 15 12:54:19 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 Sat Oct 15 2011 at 12:54:19 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3159 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5814239 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): -43.17500 18.05400 ymin,ymax (A): -55.13100 0.8600000 zmin,zma (A): -90.83500 -31.43000 x,y,z range (A): 61.22900 55.99100 59.40500 scale (grids/A): 0.5814239 object centre (A): -12.56050 -27.13550 -61.13250 number of atom coordinates read : 3159 total number of charged atoms : 3015 net assigned charge : -3.499981 assigned positive charge : 464.9732 centred at (gu) : 88.78493 91.71774 88.41063 assigned negative charge : -468.4753 centred at (gu) : 88.76777 91.70600 88.49481 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7385 nv = 96 ne = 84 npr = 60529 no. pairs analyzed = 60529 no. exposed pairs = 4511 no. arc points = 33369 no. surface atoms = 1502 nbur = 1657 mkacc time = 9.9999994E-02 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= 359 mr = 3438 m= 4 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3314 ## 346 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9202 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7477124E-09 -1.9934081E-09 midg,1,midg; midg,igrid,midg -7.5566969E-10 -8.0614904E-10 1,midg,midg; igrid,midg,midg -1.6537544E-09 -3.2334477E-10 gauss-seidel spectral radius is 0.9847718 estimated iterations to convergence 67 setup time was (sec) 0.4400000 now iterating at: 12:54:19 rms-change max change #iterations 0.1002297 16.60138 at 10iterations 7.8452202E-03 1.146983 at 20iterations 6.1153475E-04 9.1109276E-02 at 30iterations 4.9645321E-05 7.2422028E-03 at 40iterations 4.6235946E-06 7.0190430E-04 at 50iterations finished qdiffx linear iterations at : 12:54:23 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 4.6235946E-06 7.0190430E-04 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 12:54:23 3.665u 0.210s 0:04.18 92.5% 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 Sat Oct 15 2011 at 12:54:23 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3159 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.744272 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): -43.17500 18.05400 ymin,ymax (A): -55.13100 0.8600000 zmin,zma (A): -90.83500 -31.43000 x,y,z range (A): 61.22900 55.99100 59.40500 scale (grids/A): 1.744272 object centre (A): -12.56050 -27.13550 -61.13250 number of atom coordinates read : 3159 total number of charged atoms : 3015 net assigned charge : -3.499981 assigned positive charge : 464.9732 centred at (gu) : 86.35377 95.15209 85.23102 assigned negative charge : -468.4753 centred at (gu) : 86.30308 95.11773 85.48402 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 79651 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33369 grid for indexing accessible points = 1.400000 m= 25351 mr = 50281 m= 3543 mr = 16720 m= 139 mr = 1851 m= 3 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 388 time to turn everything in is 0.4000000 number of dielectric boundary points 39817 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 23440 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) : 0.5814239 object centre at (A) : -12.56050 -27.13550 -61.13250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1231999E-02 -2.2653436E-02 midg,1,midg; midg,igrid,midg -1.4077798E-02 -3.9868886E-03 1,midg,midg; igrid,midg,midg -5.2040759E-03 6.4868643E-03 gauss-seidel spectral radius is 0.9984695 estimated iterations to convergence 203 setup time was (sec) 0.6300000 now iterating at: 12:54:24 rms-change max change #iterations 3.937328 198.1086 at 10iterations 1.743978 61.49087 at 20iterations 0.7788129 26.03678 at 30iterations 0.3476319 10.39132 at 40iterations 0.1553093 4.898280 at 50iterations 6.9090299E-02 2.041283 at 60iterations 3.0960210E-02 1.034203 at 70iterations 1.3804889E-02 0.4563122 at 80iterations 6.1861062E-03 0.2284241 at 90iterations 2.7569416E-03 9.6170835E-02 at 100iterations 1.2409706E-03 4.0569305E-02 at 110iterations 5.5302918E-04 2.0114899E-02 at 120iterations finished qdiffx linear iterations at : 12:54:34 total time elapsed so far: 8.210000 # loops : 120 mean,max change (kT/e) : 5.5302918E-04 2.0114899E-02 energy calculations done at 8.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.340000 DelPhi exited at 12:54:34 8.343u 0.245s 0:11.09 77.3% 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 Sat Oct 15 2011 at 12:54:34 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3159 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.616407 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): -43.17500 18.05400 ymin,ymax (A): -55.13100 0.8600000 zmin,zma (A): -90.83500 -31.43000 x,y,z range (A): 61.22900 55.99100 59.40500 scale (grids/A): 2.616407 object centre (A): -12.56050 -27.13550 -61.13250 number of atom coordinates read : 3159 total number of charged atoms : 3015 net assigned charge : -3.499981 assigned positive charge : 464.9732 centred at (gu) : 84.53035 97.72787 82.84631 assigned negative charge : -468.4753 centred at (gu) : 84.45448 97.67656 83.22596 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 184404 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33369 grid for indexing accessible points = 1.400000 m= 83572 mr = 123873 m= 27561 mr = 63839 m= 5835 mr = 20306 m= 613 mr = 3934 m= 12 mr = 304 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 1268 time to turn everything in is 0.9900000 number of dielectric boundary points 89741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 24112 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) : 1.744272 object centre at (A) : -12.56050 -27.13550 -61.13250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1758114 -0.3728166 midg,1,midg; midg,igrid,midg -0.2480755 -5.6566190E-02 1,midg,midg; igrid,midg,midg -7.5065255E-02 8.9070223E-02 gauss-seidel spectral radius is 0.9992411 estimated iterations to convergence 287 setup time was (sec) 1.250000 now iterating at: 12:54:36 rms-change max change #iterations 9.989055 314.2565 at 10iterations 5.918818 153.1898 at 20iterations 3.453698 82.03782 at 30iterations 2.015958 45.62488 at 40iterations 1.167763 25.03192 at 50iterations 0.6737981 13.11730 at 60iterations 0.3876314 8.263824 at 70iterations 0.2225163 4.684757 at 80iterations 0.1277978 2.497898 at 90iterations 7.3185138E-02 1.295197 at 100iterations 4.1831195E-02 0.7588499 at 110iterations 2.3994185E-02 0.4256363 at 120iterations 1.3691700E-02 0.2510719 at 130iterations 7.8198090E-03 0.1452827 at 140iterations 4.4827834E-03 8.3874702E-02 at 150iterations 2.5491538E-03 4.9502373E-02 at 160iterations 1.4556465E-03 2.6258945E-02 at 170iterations 8.3275599E-04 1.6170502E-02 at 180iterations finished qdiffx linear iterations at : 12:54:48 total time elapsed so far: 13.38000 # loops : 180 mean,max change (kT/e) : 8.3275599E-04 1.6170502E-02 energy calculations done at 13.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.51000 DelPhi exited at 12:54:49 13.515u 0.255s 0:14.67 93.7% 0+0k 0+0io 0pf+0w