Sat Oct 8 21:05:47 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 8 2011 at 21:05:47 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! WARNING: HIR 91 has a net charge of 0.5140 !!! WARNING: HIR 93 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6142273 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): -10.40100 38.58500 ymin,ymax (A): -21.88200 25.13000 zmin,zma (A): -12.48100 45.47800 x,y,z range (A): 48.98600 47.01200 57.95900 scale (grids/A): 0.6142273 object centre (A): 14.09200 1.624000 16.49850 number of atom coordinates read : 2573 total number of charged atoms : 2453 net assigned charge : 3.528004 assigned positive charge : 392.4880 centred at (gu) : 88.53434 89.12373 89.52385 assigned negative charge : -388.9606 centred at (gu) : 88.42438 89.15846 89.42463 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6289 nv = 96 ne = 84 npr = 53519 no. pairs analyzed = 53519 no. exposed pairs = 3052 no. arc points = 21697 no. surface atoms = 1021 nbur = 1552 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 293 mr = 3454 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.1900000 number of dielectric boundary points 3102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2208 ## 252 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7894 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5092911E-09 7.1859403E-09 midg,1,midg; midg,igrid,midg 5.3756350E-09 4.5839624E-10 1,midg,midg; igrid,midg,midg -5.3052331E-09 6.2021255E-09 gauss-seidel spectral radius is 0.9862691 estimated iterations to convergence 70 setup time was (sec) 0.4100000 now iterating at: 21:05:48 rms-change max change #iterations 0.1189394 18.09999 at 10iterations 1.0816481E-02 1.723022 at 20iterations 9.5439272E-04 0.1463470 at 30iterations 9.1067806E-05 1.7156601E-02 at 40iterations 8.8532715E-06 1.5830994E-03 at 50iterations finished qdiffx linear iterations at : 21:05:51 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 8.8532715E-06 1.5830994E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 21:05:51 3.604u 0.206s 0:04.10 92.6% 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 Sat Oct 8 2011 at 21:05:51 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! WARNING: HIR 91 has a net charge of 0.5140 !!! WARNING: HIR 93 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.842682 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): -10.40100 38.58500 ymin,ymax (A): -21.88200 25.13000 zmin,zma (A): -12.48100 45.47800 x,y,z range (A): 48.98600 47.01200 57.95900 scale (grids/A): 1.842682 object centre (A): 14.09200 1.624000 16.49850 number of atom coordinates read : 2573 total number of charged atoms : 2453 net assigned charge : 3.528004 assigned positive charge : 392.4880 centred at (gu) : 85.60233 87.37064 88.57114 assigned negative charge : -388.9606 centred at (gu) : 85.27299 87.47528 88.27352 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21697 grid for indexing accessible points = 1.400000 m= 22989 mr = 47504 m= 3044 mr = 16729 m= 139 mr = 1768 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 3816 time to turn everything in is 0.3400000 number of dielectric boundary points 28623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19222 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) : 0.6142273 object centre at (A) : 14.09200 1.624000 16.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5794601E-02 1.6892785E-02 midg,1,midg; midg,igrid,midg 1.1331432E-02 3.3416913E-03 1,midg,midg; igrid,midg,midg -5.7219812E-03 3.3501681E-02 gauss-seidel spectral radius is 0.9985374 estimated iterations to convergence 207 setup time was (sec) 0.5800000 now iterating at: 21:05:52 rms-change max change #iterations 3.946222 179.7248 at 10iterations 1.795065 62.88752 at 20iterations 0.8191380 27.42311 at 30iterations 0.3737452 13.18111 at 40iterations 0.1702825 5.855438 at 50iterations 7.7748589E-02 2.670391 at 60iterations 3.5395682E-02 1.215667 at 70iterations 1.6222559E-02 0.5212269 at 80iterations 7.3822136E-03 0.2715147 at 90iterations 3.3645511E-03 0.1155720 at 100iterations 1.5386165E-03 5.2394629E-02 at 110iterations 7.0150226E-04 2.1789849E-02 at 120iterations finished qdiffx linear iterations at : 21:06:00 total time elapsed so far: 8.290000 # loops : 120 mean,max change (kT/e) : 7.0150226E-04 2.1789849E-02 energy calculations done at 8.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.430000 DelPhi exited at 21:06:00 8.430u 0.246s 0:09.02 96.1% 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 Sat Oct 8 2011 at 21:06:00 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! WARNING: HIR 91 has a net charge of 0.5140 !!! WARNING: HIR 93 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.764023 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): -10.40100 38.58500 ymin,ymax (A): -21.88200 25.13000 zmin,zma (A): -12.48100 45.47800 x,y,z range (A): 48.98600 47.01200 57.95900 scale (grids/A): 2.764023 object centre (A): 14.09200 1.624000 16.49850 number of atom coordinates read : 2573 total number of charged atoms : 2453 net assigned charge : 3.528004 assigned positive charge : 392.4880 centred at (gu) : 83.40346 86.05578 87.85654 assigned negative charge : -388.9606 centred at (gu) : 82.90945 86.21282 87.41032 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 159016 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21697 grid for indexing accessible points = 1.400000 m= 77245 mr = 115615 m= 25004 mr = 63036 m= 5271 mr = 19755 m= 580 mr = 3802 m= 30 mr = 350 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 12809 time to turn everything in is 0.8600000 number of dielectric boundary points 64574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 19623 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) : 1.842682 object centre at (A) : 14.09200 1.624000 16.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1094090 0.2168734 midg,1,midg; midg,igrid,midg 0.1612089 1.6193667E-02 1,midg,midg; igrid,midg,midg -7.9851031E-02 0.4553760 gauss-seidel spectral radius is 0.9992263 estimated iterations to convergence 284 setup time was (sec) 1.110000 now iterating at: 21:06:01 rms-change max change #iterations 9.295288 280.7482 at 10iterations 5.324550 148.3327 at 20iterations 3.019633 70.97713 at 30iterations 1.722811 36.79998 at 40iterations 0.9766453 20.04189 at 50iterations 0.5538546 10.47225 at 60iterations 0.3147510 6.290699 at 70iterations 0.1783389 3.629025 at 80iterations 0.1011550 1.979006 at 90iterations 5.7459984E-02 1.111202 at 100iterations 3.2506794E-02 0.6494083 at 110iterations 1.8381147E-02 0.3447670 at 120iterations 1.0442832E-02 0.2271423 at 130iterations 5.9270300E-03 0.1261921 at 140iterations 3.3564791E-03 6.1464310E-02 at 150iterations 1.9053436E-03 3.7631989E-02 at 160iterations 1.0823975E-03 2.1732807E-02 at 170iterations 6.1510282E-04 1.1516571E-02 at 180iterations finished qdiffx linear iterations at : 21:06:13 total time elapsed so far: 13.18000 # loops : 180 mean,max change (kT/e) : 6.1510282E-04 1.1516571E-02 energy calculations done at 13.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 21:06:14 13.311u 0.222s 0:13.80 98.0% 0+0k 0+0io 0pf+0w