Sun Oct 9 13:42:51 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+sph.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 = amb.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 13:42:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 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: 0.7014502 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): -6.728000 44.02400 ymin,ymax (A): -14.13400 35.83500 zmin,zma (A): 1.668000 44.52100 x,y,z range (A): 50.75200 49.96900 42.85300 scale (grids/A): 0.7014502 object centre (A): 18.64800 10.85050 23.09450 number of atom coordinates read : 2383 total number of charged atoms : 2243 net assigned charge : 4.500011 assigned positive charge : 363.1791 centred at (gu) : 89.73142 91.44905 90.92324 assigned negative charge : -358.6796 centred at (gu) : 89.72913 91.60771 91.04135 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7970 nv = 96 ne = 84 npr = 47835 no. pairs analyzed = 47835 no. exposed pairs = 2986 no. arc points = 21176 no. surface atoms = 1011 nbur = 1372 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 510 mr = 4432 m= 2 mr = 99 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 0.2800000 number of dielectric boundary points 3951 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1898 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8892 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7276667E-08 -2.9796848E-08 midg,1,midg; midg,igrid,midg 8.4409656E-08 -6.1177950E-08 1,midg,midg; igrid,midg,midg 3.5447702E-08 3.4159914E-08 gauss-seidel spectral radius is 0.9894406 estimated iterations to convergence 79 setup time was (sec) 0.5000000 now iterating at: 13:42:52 rms-change max change #iterations 0.2050499 25.38044 at 10iterations 2.5278052E-02 3.947304 at 20iterations 3.5488736E-03 0.5521584 at 30iterations 7.5266312E-04 0.1139832 at 40iterations 2.4319389E-04 3.9600372E-02 at 50iterations finished qdiffx linear iterations at : 13:42:54 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 2.4319389E-04 3.9600372E-02 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 13:42:55 3.074u 0.150s 0:03.53 91.2% 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 13:42:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 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: 2.104351 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): -6.728000 44.02400 ymin,ymax (A): -14.13400 35.83500 zmin,zma (A): 1.668000 44.52100 x,y,z range (A): 50.75200 49.96900 42.85300 scale (grids/A): 2.104351 object centre (A): 18.64800 10.85050 23.09450 number of atom coordinates read : 2383 total number of charged atoms : 2243 net assigned charge : 4.500011 assigned positive charge : 363.1791 centred at (gu) : 89.19392 94.34689 92.76903 assigned negative charge : -358.6796 centred at (gu) : 89.18718 94.82292 93.12396 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 83886 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21176 grid for indexing accessible points = 1.400000 m= 32270 mr = 58080 m= 6016 mr = 24007 m= 609 mr = 4045 m= 12 mr = 318 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 418 time to turn everything in is 0.5800000 number of dielectric boundary points 36343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17820 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) : 0.7014502 object centre at (A) : 18.64800 10.85050 23.09450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4584272E-02 1.0059468E-03 midg,1,midg; midg,igrid,midg 2.0535156E-02 -4.8281096E-02 1,midg,midg; igrid,midg,midg 5.6034196E-02 1.3636972E-03 gauss-seidel spectral radius is 0.9988511 estimated iterations to convergence 233 setup time was (sec) 0.8400000 now iterating at: 13:42:56 rms-change max change #iterations 4.936521 254.1550 at 10iterations 2.446643 83.84506 at 20iterations 1.220974 35.26293 at 30iterations 0.6090635 18.76817 at 40iterations 0.3047113 8.740551 at 50iterations 0.1517990 4.586762 at 60iterations 7.5650156E-02 2.199997 at 70iterations 3.7960492E-02 1.097410 at 80iterations 1.9033829E-02 0.5244980 at 90iterations 9.6266652E-03 0.3348951 at 100iterations 4.9160062E-03 0.1353807 at 110iterations 2.5809132E-03 7.6204300E-02 at 120iterations finished qdiffx linear iterations at : 13:43:02 total time elapsed so far: 6.850000 # loops : 120 mean,max change (kT/e) : 2.5809132E-03 7.6204300E-02 energy calculations done at 6.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.020000 DelPhi exited at 13:43:03 7.027u 0.161s 0:07.49 95.8% 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 13:43:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.156526 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): -6.728000 44.02400 ymin,ymax (A): -14.13400 35.83500 zmin,zma (A): 1.668000 44.52100 x,y,z range (A): 50.75200 49.96900 42.85300 scale (grids/A): 3.156526 object centre (A): 18.64800 10.85050 23.09450 number of atom coordinates read : 2383 total number of charged atoms : 2243 net assigned charge : 4.500011 assigned positive charge : 363.1791 centred at (gu) : 88.79070 96.52010 94.15350 assigned negative charge : -358.6796 centred at (gu) : 88.78075 97.23434 94.68581 start vw surface at 0.1500000 fill in re-entrant regions at 0.8500000 boundary points on vw surface= 193366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21176 grid for indexing accessible points = 1.400000 m= 101546 mr = 140166 m= 40132 mr = 83603 m= 11342 mr = 32620 m= 2388 mr = 8777 m= 255 mr = 1794 m= 2 mr = 166 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1297 time to turn everything in is 1.850000 number of dielectric boundary points 81905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 17944 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) : 2.104351 object centre at (A) : 18.64800 10.85050 23.09450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4817851 -8.2357772E-02 midg,1,midg; midg,igrid,midg 0.3561162 -0.5017223 1,midg,midg; igrid,midg,midg 0.6009292 -0.3536231 gauss-seidel spectral radius is 0.9993051 estimated iterations to convergence 299 setup time was (sec) 2.130000 now iterating at: 13:43:05 rms-change max change #iterations 11.03914 501.8613 at 10iterations 6.585795 129.0265 at 20iterations 3.900039 74.60204 at 30iterations 2.314308 43.13458 at 40iterations 1.370290 25.24603 at 50iterations 0.8083089 14.70964 at 60iterations 0.4760128 7.955041 at 70iterations 0.2805001 4.822880 at 80iterations 0.1649567 2.996592 at 90iterations 9.7071499E-02 1.532850 at 100iterations 5.7046961E-02 0.9458418 at 110iterations 3.3759318E-02 0.5994797 at 120iterations 2.0045450E-02 0.3399048 at 130iterations 1.2089189E-02 0.2165108 at 140iterations 7.4650762E-03 0.1435242 at 150iterations 4.7989860E-03 0.1137142 at 160iterations 3.2509251E-03 7.0041656E-02 at 170iterations 2.3577935E-03 5.0868988E-02 at 180iterations finished qdiffx linear iterations at : 13:43:14 total time elapsed so far: 11.53000 # loops : 180 mean,max change (kT/e) : 2.3577935E-03 5.0868988E-02 energy calculations done at 11.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 13:43:15 11.707u 0.184s 0:12.16 97.6% 0+0k 0+0io 0pf+0w