Tue Oct 11 03:20:31 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 Tue Oct 11 2011 at 03:20:31 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 = 3462 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SER 496 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5790783 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): -10.18400 43.06900 ymin,ymax (A): 14.67700 75.58200 zmin,zma (A): 40.12700 101.6040 x,y,z range (A): 53.25300 60.90500 61.47700 scale (grids/A): 0.5790783 object centre (A): 16.44250 45.12950 70.86550 number of atom coordinates read : 3462 total number of charged atoms : 3323 net assigned charge : -6.043967 assigned positive charge : 521.9113 centred at (gu) : 88.31670 87.62307 88.41674 assigned negative charge : -527.9567 centred at (gu) : 88.33736 87.60571 88.39183 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7612 nv = 96 ne = 84 npr = 70921 no. pairs analyzed = 70921 no. exposed pairs = 4304 no. arc points = 29968 no. surface atoms = 1438 nbur = 2024 mkacc time = 0.1200000 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 = 1.484000 m= 392 mr = 4118 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.2400000 number of dielectric boundary points 3851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3063 ## 337 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9703 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7102502E-09 -4.4805140E-10 midg,1,midg; midg,igrid,midg -2.9320635E-09 -4.8642373E-10 1,midg,midg; igrid,midg,midg -1.0636976E-09 -1.2039568E-09 gauss-seidel spectral radius is 0.9846453 estimated iterations to convergence 66 setup time was (sec) 0.4200000 now iterating at: 03:20:31 rms-change max change #iterations 0.1084783 15.99464 at 10iterations 8.7538101E-03 1.351147 at 20iterations 7.8444555E-04 0.1025486 at 30iterations 1.1803373E-04 1.2699127E-02 at 40iterations 2.6534755E-05 2.5024414E-03 at 50iterations finished qdiffx linear iterations at : 03:20:34 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.6534755E-05 2.5024414E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 03:20:35 3.422u 0.194s 0:04.08 88.4% 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 Tue Oct 11 2011 at 03:20:35 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 = 3462 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SER 496 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.737235 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): -10.18400 43.06900 ymin,ymax (A): 14.67700 75.58200 zmin,zma (A): 40.12700 101.6040 x,y,z range (A): 53.25300 60.90500 61.47700 scale (grids/A): 1.737235 object centre (A): 16.44250 45.12950 70.86550 number of atom coordinates read : 3462 total number of charged atoms : 3323 net assigned charge : -6.043967 assigned positive charge : 521.9113 centred at (gu) : 84.94918 82.86879 85.24940 assigned negative charge : -527.9567 centred at (gu) : 85.01154 82.81657 85.17496 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29968 grid for indexing accessible points = 1.400000 m= 29367 mr = 56587 m= 3824 mr = 21449 m= 152 mr = 2125 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1218 time to turn everything in is 0.4200000 number of dielectric boundary points 35618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 288 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 25732 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) : 0.5790783 object centre at (A) : 16.44250 45.12950 70.86550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0992745E-02 4.0648803E-02 midg,1,midg; midg,igrid,midg -1.2723505E-02 4.7859871E-03 1,midg,midg; igrid,midg,midg -3.2253854E-03 -4.7224679E-04 gauss-seidel spectral radius is 0.9984401 estimated iterations to convergence 201 setup time was (sec) 0.6500000 now iterating at: 03:20:36 rms-change max change #iterations 4.171524 155.8532 at 10iterations 1.841096 75.81218 at 20iterations 0.8188380 30.94058 at 30iterations 0.3634214 12.88494 at 40iterations 0.1616016 5.354000 at 50iterations 7.1728148E-02 2.139957 at 60iterations 3.1930409E-02 1.060413 at 70iterations 1.4189166E-02 0.4624896 at 80iterations 6.3361158E-03 0.1983948 at 90iterations 2.8289764E-03 9.6152350E-02 at 100iterations 1.2629048E-03 3.9830208E-02 at 110iterations 5.6931627E-04 1.7971158E-02 at 120iterations finished qdiffx linear iterations at : 03:20:43 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 5.6931627E-04 1.7971158E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 03:20:43 7.874u 0.195s 0:08.67 92.9% 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 Oct 11 2011 at 03:20:44 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 = 3462 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SER 496 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: 2.605853 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): -10.18400 43.06900 ymin,ymax (A): 14.67700 75.58200 zmin,zma (A): 40.12700 101.6040 x,y,z range (A): 53.25300 60.90500 61.47700 scale (grids/A): 2.605853 object centre (A): 16.44250 45.12950 70.86550 number of atom coordinates read : 3462 total number of charged atoms : 3323 net assigned charge : -6.043967 assigned positive charge : 521.9113 centred at (gu) : 82.42365 79.30288 82.87381 assigned negative charge : -527.9567 centred at (gu) : 82.51723 79.22458 82.76229 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 190742 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29968 grid for indexing accessible points = 1.400000 m= 95361 mr = 137401 m= 32946 mr = 77353 m= 6513 mr = 26217 m= 640 mr = 4610 m= 30 mr = 344 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 4344 time to turn everything in is 1.020000 number of dielectric boundary points 80307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 26570 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) : 1.737235 object centre at (A) : 16.44250 45.12950 70.86550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3927010 0.8873775 midg,1,midg; midg,igrid,midg -0.2996600 0.2641470 1,midg,midg; igrid,midg,midg -3.2751360E-03 -1.4682334E-02 gauss-seidel spectral radius is 0.9992261 estimated iterations to convergence 284 setup time was (sec) 1.270000 now iterating at: 03:20:46 rms-change max change #iterations 10.27922 323.1095 at 10iterations 5.969810 174.8779 at 20iterations 3.433920 78.13853 at 30iterations 1.973407 44.24857 at 40iterations 1.127718 25.72594 at 50iterations 0.6437866 13.45065 at 60iterations 0.3664988 7.204758 at 70iterations 0.2097512 4.723917 at 80iterations 0.1193331 2.222931 at 90iterations 6.7962997E-02 1.427474 at 100iterations 3.8649801E-02 0.7399435 at 110iterations 2.1975989E-02 0.4014015 at 120iterations 1.2489178E-02 0.2172320 at 130iterations 7.0984387E-03 0.1262565 at 140iterations 4.0458259E-03 8.2597017E-02 at 150iterations 2.3072460E-03 4.9722672E-02 at 160iterations 1.3121786E-03 2.2508621E-02 at 170iterations 7.5217296E-04 1.3717651E-02 at 180iterations finished qdiffx linear iterations at : 03:20:57 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 7.5217296E-04 1.3717651E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 03:20:58 12.877u 0.255s 0:13.65 96.1% 0+0k 0+0io 0pf+0w