Mon Oct 10 17:00:50 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 Mon Oct 10 2011 at 17:00:50 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 = 3202 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 0.5856997 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): -25.61400 32.46000 ymin,ymax (A): -8.680000 43.53500 zmin,zma (A): 6.628000 67.41000 x,y,z range (A): 58.07400 52.21500 60.78201 scale (grids/A): 0.5856997 object centre (A): 3.422999 17.42750 37.01900 number of atom coordinates read : 3202 total number of charged atoms : 3059 net assigned charge : -5.271958 assigned positive charge : 480.1105 centred at (gu) : 90.19621 88.56168 91.20512 assigned negative charge : -485.3839 centred at (gu) : 90.27040 88.41532 91.31440 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7297 nv = 96 ne = 84 npr = 64064 no. pairs analyzed = 64064 no. exposed pairs = 4211 no. arc points = 29648 no. surface atoms = 1410 nbur = 1792 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 = 1.512000 m= 335 mr = 3766 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2200000 number of dielectric boundary points 3850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3040 ## 324 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9291 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3703327E-09 -5.9283147E-09 midg,1,midg; midg,igrid,midg -7.8188327E-09 2.0365523E-09 1,midg,midg; igrid,midg,midg 8.0531443E-10 -3.5942944E-09 gauss-seidel spectral radius is 0.9849765 estimated iterations to convergence 67 setup time was (sec) 0.4400000 now iterating at: 17:00:50 rms-change max change #iterations 0.1081000 16.26641 at 10iterations 8.5094646E-03 1.284504 at 20iterations 6.8379188E-04 0.1093826 at 30iterations 5.9187238E-05 9.1400146E-03 at 40iterations 6.5577046E-06 1.2044907E-03 at 50iterations finished qdiffx linear iterations at : 17:00:53 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 6.5577046E-06 1.2044907E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 17:00:54 3.563u 0.258s 0:04.51 84.4% 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 Mon Oct 10 2011 at 17:00:54 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 = 3202 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 1.757099 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): -25.61400 32.46000 ymin,ymax (A): -8.680000 43.53500 zmin,zma (A): 6.628000 67.41000 x,y,z range (A): 58.07400 52.21500 60.78201 scale (grids/A): 1.757099 object centre (A): 3.422999 17.42750 37.01900 number of atom coordinates read : 3202 total number of charged atoms : 3059 net assigned charge : -5.271958 assigned positive charge : 480.1105 centred at (gu) : 90.58775 85.68424 93.61437 assigned negative charge : -485.3839 centred at (gu) : 90.81078 85.24562 93.94272 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80126 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29648 grid for indexing accessible points = 1.400000 m= 25824 mr = 54135 m= 3105 mr = 17911 m= 121 mr = 1609 m= 0 mr = 23 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 461 time to turn everything in is 0.4000000 number of dielectric boundary points 35498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 244 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 23783 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) : 0.5856997 object centre at (A) : 3.422999 17.42750 37.01900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9849697E-02 9.8830564E-03 midg,1,midg; midg,igrid,midg -4.1742459E-02 3.4183173E-03 1,midg,midg; igrid,midg,midg 1.1625576E-02 -3.7044525E-02 gauss-seidel spectral radius is 0.9984646 estimated iterations to convergence 202 setup time was (sec) 0.6400000 now iterating at: 17:00:55 rms-change max change #iterations 4.062204 157.4166 at 10iterations 1.800249 56.69267 at 20iterations 0.8056787 27.27669 at 30iterations 0.3590486 10.75711 at 40iterations 0.1605820 5.425638 at 50iterations 7.1699858E-02 2.217312 at 60iterations 3.2067962E-02 1.108189 at 70iterations 1.4336116E-02 0.4466839 at 80iterations 6.4292373E-03 0.2269862 at 90iterations 2.8742086E-03 8.7384701E-02 at 100iterations 1.2897941E-03 4.7029495E-02 at 110iterations 5.7582080E-04 2.0332336E-02 at 120iterations finished qdiffx linear iterations at : 17:01:03 total time elapsed so far: 8.520000 # loops : 120 mean,max change (kT/e) : 5.7582080E-04 2.0332336E-02 energy calculations done at 8.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.650000 DelPhi exited at 17:01:04 8.655u 0.266s 0:09.78 91.1% 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 Mon Oct 10 2011 at 17:01:04 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 = 3202 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 2.635648 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): -25.61400 32.46000 ymin,ymax (A): -8.680000 43.53500 zmin,zma (A): 6.628000 67.41000 x,y,z range (A): 58.07400 52.21500 60.78201 scale (grids/A): 2.635648 object centre (A): 3.422999 17.42750 37.01900 number of atom coordinates read : 3202 total number of charged atoms : 3059 net assigned charge : -5.271958 assigned positive charge : 480.1105 centred at (gu) : 90.88139 83.52609 95.42116 assigned negative charge : -485.3839 centred at (gu) : 91.21616 82.86816 95.91397 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 185850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29648 grid for indexing accessible points = 1.400000 m= 87107 mr = 132315 m= 27378 mr = 68804 m= 4989 mr = 20756 m= 452 mr = 3406 m= 19 mr = 209 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 1440 time to turn everything in is 1.020000 number of dielectric boundary points 80305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 24462 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) : 1.757099 object centre at (A) : 3.422999 17.42750 37.01900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5140154 0.2199195 midg,1,midg; midg,igrid,midg -0.4810127 4.3746267E-02 1,midg,midg; igrid,midg,midg 0.2549040 -0.4595004 gauss-seidel spectral radius is 0.9992328 estimated iterations to convergence 285 setup time was (sec) 1.290000 now iterating at: 17:01:06 rms-change max change #iterations 10.10606 309.4213 at 10iterations 5.896556 150.7521 at 20iterations 3.410338 73.15791 at 30iterations 1.964124 41.19474 at 40iterations 1.125530 24.07257 at 50iterations 0.6463293 14.47137 at 60iterations 0.3693372 7.534500 at 70iterations 0.2112226 4.140477 at 80iterations 0.1203899 2.298708 at 90iterations 6.8472259E-02 1.321075 at 100iterations 3.8968097E-02 0.7058048 at 110iterations 2.2208607E-02 0.3960667 at 120iterations 1.2673905E-02 0.2554216 at 130iterations 7.1791643E-03 0.1255016 at 140iterations 4.0923087E-03 7.9312325E-02 at 150iterations 2.3271111E-03 4.2059183E-02 at 160iterations 1.3236599E-03 2.4425030E-02 at 170iterations 7.5326639E-04 1.3917923E-02 at 180iterations finished qdiffx linear iterations at : 17:01:18 total time elapsed so far: 13.78000 # loops : 180 mean,max change (kT/e) : 7.5326639E-04 1.3917923E-02 energy calculations done at 13.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.90000 DelPhi exited at 17:01:19 13.906u 0.315s 0:15.19 93.5% 0+0k 0+0io 0pf+0w