Tue Nov 22 14:12:05 PST 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 Tue Nov 22 2011 at 14:12:10 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6423094 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): -5.261000 33.91900 ymin,ymax (A): -3.425000 47.55300 zmin,zma (A): -8.060000 47.36500 x,y,z range (A): 39.18000 50.97800 55.42500 scale (grids/A): 0.6423094 object centre (A): 14.32900 22.06400 19.65250 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000011 assigned positive charge : 290.9620 centred at (gu) : 89.64522 92.66043 89.89197 assigned negative charge : -285.9623 centred at (gu) : 89.57111 92.76306 89.94744 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5517 nv = 96 ne = 84 npr = 40207 no. pairs analyzed = 40207 no. exposed pairs = 2473 no. arc points = 17204 no. surface atoms = 835 nbur = 1123 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 270 mr = 3050 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.1600000 number of dielectric boundary points 2689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1765 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6550 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3325799E-08 2.9029594E-09 midg,1,midg; midg,igrid,midg 9.8867226E-09 -2.9544480E-09 1,midg,midg; igrid,midg,midg 1.3130363E-09 1.3633326E-08 gauss-seidel spectral radius is 0.9873846 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 14:12:13 rms-change max change #iterations 0.1300492 19.49714 at 10iterations 1.2628026E-02 2.240788 at 20iterations 1.2547706E-03 0.2036057 at 30iterations 1.2506935E-04 1.9212723E-02 at 40iterations 1.2496372E-05 2.0637512E-03 at 50iterations finished qdiffx linear iterations at : 14:12:23 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 1.2496372E-05 2.0637512E-03 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.900000 DelPhi exited at 14:12:25 3.899u 0.251s 0:15.99 25.8% 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 Tue Nov 22 2011 at 14:12:27 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.926928 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): -5.261000 33.91900 ymin,ymax (A): -3.425000 47.55300 zmin,zma (A): -8.060000 47.36500 x,y,z range (A): 39.18000 50.97800 55.42500 scale (grids/A): 1.926928 object centre (A): 14.32900 22.06400 19.65250 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000011 assigned positive charge : 290.9620 centred at (gu) : 88.93568 97.98132 89.67578 assigned negative charge : -285.9623 centred at (gu) : 88.71358 98.28937 89.84235 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59438 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17204 grid for indexing accessible points = 1.400000 m= 21126 mr = 40981 m= 2949 mr = 16069 m= 147 mr = 1853 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 3258 time to turn everything in is 0.3100000 number of dielectric boundary points 24713 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14379 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) : 0.6423094 object centre at (A) : 14.32900 22.06400 19.65250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0987518E-02 3.9997876E-02 midg,1,midg; midg,igrid,midg 3.2248989E-02 7.3939661E-04 1,midg,midg; igrid,midg,midg 7.8271655E-03 7.1161422E-03 gauss-seidel spectral radius is 0.9985864 estimated iterations to convergence 211 setup time was (sec) 0.5700000 now iterating at: 14:12:32 rms-change max change #iterations 3.708126 168.3769 at 10iterations 1.714743 69.00765 at 20iterations 0.7948815 28.38763 at 30iterations 0.3662595 13.60441 at 40iterations 0.1692194 6.238492 at 50iterations 7.8126028E-02 2.919091 at 60iterations 3.5986919E-02 1.286131 at 70iterations 1.6689172E-02 0.5764465 at 80iterations 7.6763360E-03 0.2672076 at 90iterations 3.5546587E-03 0.1372585 at 100iterations 1.6429871E-03 5.6373596E-02 at 110iterations 7.5880735E-04 2.7095795E-02 at 120iterations finished qdiffx linear iterations at : 14:12:57 total time elapsed so far: 8.780000 # loops : 120 mean,max change (kT/e) : 7.5880735E-04 2.7095795E-02 energy calculations done at 8.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.920000 DelPhi exited at 14:12:58 8.918u 0.267s 0:31.00 29.5% 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 Tue Nov 22 2011 at 14:13:01 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.890392 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): -5.261000 33.91900 ymin,ymax (A): -3.425000 47.55300 zmin,zma (A): -8.060000 47.36500 x,y,z range (A): 39.18000 50.97800 55.42500 scale (grids/A): 2.890392 object centre (A): 14.32900 22.06400 19.65250 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000011 assigned positive charge : 290.9620 centred at (gu) : 88.40343 101.9720 89.51380 assigned negative charge : -285.9623 centred at (gu) : 88.07040 102.4342 89.76354 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 137515 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17204 grid for indexing accessible points = 1.400000 m= 69226 mr = 99435 m= 24336 mr = 57349 m= 5141 mr = 20058 m= 657 mr = 3890 m= 22 mr = 447 m= 0 mr = 9 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 11426 time to turn everything in is 0.8000000 number of dielectric boundary points 55709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 14608 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) : 1.926928 object centre at (A) : 14.32900 22.06400 19.65250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2215821E-02 0.9649532 midg,1,midg; midg,igrid,midg 0.3622001 -3.3027031E-02 1,midg,midg; igrid,midg,midg 0.1321857 3.9040986E-02 gauss-seidel spectral radius is 0.9992321 estimated iterations to convergence 285 setup time was (sec) 1.060000 now iterating at: 14:13:07 rms-change max change #iterations 8.657662 390.7872 at 10iterations 4.961101 131.2736 at 20iterations 2.821976 63.43393 at 30iterations 1.601374 33.06318 at 40iterations 0.9085957 18.55425 at 50iterations 0.5171691 10.40683 at 60iterations 0.2930418 5.916637 at 70iterations 0.1660243 3.694242 at 80iterations 9.4388105E-02 1.969039 at 90iterations 5.3515092E-02 1.044924 at 100iterations 3.0371111E-02 0.6088142 at 110iterations 1.7222330E-02 0.3395786 at 120iterations 9.7680418E-03 0.1829453 at 130iterations 5.5224365E-03 0.1197901 at 140iterations 3.1475201E-03 6.0690403E-02 at 150iterations 1.7844532E-03 3.4991264E-02 at 160iterations 1.0137063E-03 2.0803213E-02 at 170iterations 5.7512440E-04 1.1120796E-02 at 180iterations finished qdiffx linear iterations at : 14:13:45 total time elapsed so far: 13.86000 # loops : 180 mean,max change (kT/e) : 5.7512440E-04 1.1120796E-02 energy calculations done at 13.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.00000 DelPhi exited at 14:13:47 14.001u 0.266s 0:47.10 30.2% 0+0k 0+0io 0pf+0w