Wed Feb 15 08:54:36 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3286 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: 0.5976765 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): 51.60600 111.1700 ymin,ymax (A): -18.89500 40.56100 zmin,zma (A): -34.33900 24.43900 x,y,z range (A): 59.56400 59.45600 58.77800 scale (grids/A): 0.5976765 object centre (A): 81.38800 10.83300 -4.950001 number of atom coordinates read : 3286 total number of charged atoms : 3145 net assigned charge : 4.000026 assigned positive charge : 488.5426 centred at (gu) : 88.05870 89.59211 91.75639 assigned negative charge : -484.5439 centred at (gu) : 88.05456 89.72458 91.76156 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7912 nv = 96 ne = 84 npr = 66565 no. pairs analyzed = 66565 no. exposed pairs = 4380 no. arc points = 30772 no. surface atoms = 1453 nbur = 1833 mkacc time = 0.1100000 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 = 1.456000 m= 380 mr = 4063 m= 0 mr = 30 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.2500000 number of dielectric boundary points 4199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3113 ## 288 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 9885 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2102729E-09 1.9799069E-09 midg,1,midg; midg,igrid,midg 7.7379321E-09 -3.7172772E-09 1,midg,midg; igrid,midg,midg 2.1316158E-09 1.1350627E-09 gauss-seidel spectral radius is 0.9855772 estimated iterations to convergence 68 setup time was (sec) 0.4700000 now iterating at: 08:54:37 rms-change max change #iterations 0.1200818 17.90665 at 10iterations 1.1224784E-02 1.579697 at 20iterations 1.8337299E-03 0.3082428 at 30iterations 5.4851273E-04 9.1392517E-02 at 40iterations 1.8196332E-04 3.0307770E-02 at 50iterations finished qdiffx linear iterations at : 08:54:40 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.8196332E-04 3.0307770E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 08:54:41 3.529u 0.240s 0:04.52 83.1% 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 Wed Feb 15 2012 at 08:54:41 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 = 3286 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: 1.793029 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): 51.60600 111.1700 ymin,ymax (A): -18.89500 40.56100 zmin,zma (A): -34.33900 24.43900 x,y,z range (A): 59.56400 59.45600 58.77800 scale (grids/A): 1.793029 object centre (A): 81.38800 10.83300 -4.950001 number of atom coordinates read : 3286 total number of charged atoms : 3145 net assigned charge : 4.000026 assigned positive charge : 488.5426 centred at (gu) : 84.17544 88.77509 95.26852 assigned negative charge : -484.5439 centred at (gu) : 84.16328 89.17319 95.28426 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30772 grid for indexing accessible points = 1.400000 m= 29137 mr = 57028 m= 4121 mr = 20404 m= 189 mr = 2442 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 2588 time to turn everything in is 0.4300000 number of dielectric boundary points 38573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 233 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 24560 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) : 0.5976765 object centre at (A) : 81.38800 10.83300 -4.950001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1590107E-02 2.2501612E-02 midg,1,midg; midg,igrid,midg 1.8321749E-02 -2.8465804E-02 1,midg,midg; igrid,midg,midg 1.1470421E-02 1.6957928E-03 gauss-seidel spectral radius is 0.9985344 estimated iterations to convergence 207 setup time was (sec) 0.6900000 now iterating at: 08:54:42 rms-change max change #iterations 4.255953 168.1847 at 10iterations 1.923165 67.49159 at 20iterations 0.8758138 31.27402 at 30iterations 0.3994468 12.68066 at 40iterations 0.1819442 5.379654 at 50iterations 8.2766004E-02 2.470701 at 60iterations 3.7829380E-02 1.120968 at 70iterations 1.7485520E-02 0.5611258 at 80iterations 8.1326608E-03 0.2453623 at 90iterations 3.8940879E-03 0.1355362 at 100iterations 1.9481312E-03 6.6326141E-02 at 110iterations 1.0251228E-03 3.5247803E-02 at 120iterations finished qdiffx linear iterations at : 08:54:50 total time elapsed so far: 8.480000 # loops : 120 mean,max change (kT/e) : 1.0251228E-03 3.5247803E-02 energy calculations done at 8.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.610000 DelPhi exited at 08:54:57 8.616u 0.299s 0:15.44 57.6% 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 Wed Feb 15 2012 at 08:54:57 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 = 3286 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: 2.689544 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): 51.60600 111.1700 ymin,ymax (A): -18.89500 40.56100 zmin,zma (A): -34.33900 24.43900 x,y,z range (A): 59.56400 59.45600 58.77800 scale (grids/A): 2.689544 object centre (A): 81.38800 10.83300 -4.950001 number of atom coordinates read : 3286 total number of charged atoms : 3145 net assigned charge : 4.000026 assigned positive charge : 488.5426 centred at (gu) : 81.26282 88.16242 97.90240 assigned negative charge : -484.5439 centred at (gu) : 81.24470 88.75964 97.92641 start vw surface at 0.1000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 196910 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30772 grid for indexing accessible points = 1.400000 m= 95550 mr = 139075 m= 32642 mr = 75834 m= 7100 mr = 25361 m= 836 mr = 5225 m= 30 mr = 500 m= 0 mr = 2 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 9058 time to turn everything in is 1.140000 number of dielectric boundary points 87071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 25150 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) : 1.793029 object centre at (A) : 81.38800 10.83300 -4.950001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1425903 0.1882512 midg,1,midg; midg,igrid,midg 0.2388846 -0.3363808 1,midg,midg; igrid,midg,midg 0.4763887 -3.0391913E-02 gauss-seidel spectral radius is 0.9992534 estimated iterations to convergence 289 setup time was (sec) 1.430000 now iterating at: 08:54:59 rms-change max change #iterations 10.58824 389.6960 at 10iterations 6.327333 161.9152 at 20iterations 3.732971 79.26896 at 30iterations 2.185359 45.80408 at 40iterations 1.276774 24.54553 at 50iterations 0.7398118 15.34212 at 60iterations 0.4302158 8.445610 at 70iterations 0.2486856 4.884627 at 80iterations 0.1435474 2.554739 at 90iterations 8.2938008E-02 1.451469 at 100iterations 4.7716081E-02 0.8690988 at 110iterations 2.7518868E-02 0.4761333 at 120iterations 1.5883813E-02 0.2726364 at 130iterations 9.1668870E-03 0.1714482 at 140iterations 5.3083980E-03 9.6343994E-02 at 150iterations 3.0981670E-03 5.9295654E-02 at 160iterations 1.8285975E-03 3.6277771E-02 at 170iterations 1.0977455E-03 2.2621155E-02 at 180iterations finished qdiffx linear iterations at : 08:55:11 total time elapsed so far: 14.15000 # loops : 180 mean,max change (kT/e) : 1.0977455E-03 2.2621155E-02 energy calculations done at 14.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.28000 DelPhi exited at 08:55:12 14.281u 0.321s 0:14.94 97.7% 0+0k 0+0io 0pf+0w