Mon Oct 10 14:25:09 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 Mon Oct 10 2011 at 14:25:09 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3060 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.4795323 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): -15.74700 36.44500 ymin,ymax (A): -13.36200 60.87700 zmin,zma (A): 19.09600 76.69901 x,y,z range (A): 52.19200 74.23900 57.60300 scale (grids/A): 0.4795323 object centre (A): 10.34900 23.75750 47.89750 number of atom coordinates read : 3060 total number of charged atoms : 2911 net assigned charge : -0.4999888 assigned positive charge : 457.2702 centred at (gu) : 90.08906 90.93270 91.92307 assigned negative charge : -457.7713 centred at (gu) : 90.02029 91.01428 91.89447 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4543 nv = 96 ne = 84 npr = 59000 no. pairs analyzed = 59000 no. exposed pairs = 4405 no. arc points = 31572 no. surface atoms = 1455 nbur = 1605 mkacc time = 0.1300000 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 = 1.764000 m= 181 mr = 1970 m= 0 mr = 2 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2752 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3002 ## 581 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6193 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.6409799E-12 1.7287042E-11 midg,1,midg; midg,igrid,midg 2.3734842E-11 -4.5241273E-11 1,midg,midg; igrid,midg,midg -2.8697494E-11 2.6505515E-11 gauss-seidel spectral radius is 0.9776770 estimated iterations to convergence 56 setup time was (sec) 0.5100000 now iterating at: 14:25:10 rms-change max change #iterations 3.8337134E-02 9.374328 at 10iterations 1.7795728E-03 0.3493958 at 20iterations 8.8395282E-05 2.0774841E-02 at 30iterations 6.4509945E-06 1.9741058E-03 at 40iterations 7.7529359E-07 2.4795532E-04 at 50iterations finished qdiffx linear iterations at : 14:25:12 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 7.7529359E-07 2.4795532E-04 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 14:25:13 3.149u 0.174s 0:03.77 87.7% 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 14:25:13 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3060 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.438597 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): -15.74700 36.44500 ymin,ymax (A): -13.36200 60.87700 zmin,zma (A): 19.09600 76.69901 x,y,z range (A): 52.19200 74.23900 57.60300 scale (grids/A): 1.438597 object centre (A): 10.34900 23.75750 47.89750 number of atom coordinates read : 3060 total number of charged atoms : 2911 net assigned charge : -0.4999888 assigned positive charge : 457.2702 centred at (gu) : 90.26651 92.79742 95.76846 assigned negative charge : -457.7713 centred at (gu) : 90.06075 93.04260 95.68323 start vw surface at 0.1700000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 50936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31572 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 12496 mr = 31133 m= 846 mr = 7222 m= 11 mr = 242 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 273 time to turn everything in is 0.4000000 number of dielectric boundary points 25693 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 491 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 21444 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) : 0.4795323 object centre at (A) : 10.34900 23.75750 47.89750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5956677E-03 1.3106376E-03 midg,1,midg; midg,igrid,midg 1.2298181E-03 -1.0913110E-02 1,midg,midg; igrid,midg,midg -1.8882403E-03 4.5969938E-03 gauss-seidel spectral radius is 0.9976560 estimated iterations to convergence 164 setup time was (sec) 0.6800000 now iterating at: 14:25:14 rms-change max change #iterations 2.501447 140.9207 at 10iterations 0.9184301 52.82338 at 20iterations 0.3386606 15.79828 at 30iterations 0.1253510 5.611072 at 40iterations 4.6100628E-02 1.902319 at 50iterations 1.7053122E-02 0.6979735 at 60iterations 6.2850979E-03 0.2769062 at 70iterations 2.3318327E-03 0.1089172 at 80iterations 8.6619693E-04 3.3870935E-02 at 90iterations 3.1985456E-04 1.4682770E-02 at 100iterations 1.1813219E-04 4.6505928E-03 at 110iterations 4.3883636E-05 2.0394325E-03 at 120iterations finished qdiffx linear iterations at : 14:25:20 total time elapsed so far: 6.600000 # loops : 120 mean,max change (kT/e) : 4.3883636E-05 2.0394325E-03 energy calculations done at 6.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.800000 DelPhi exited at 14:25:20 6.799u 0.206s 0:07.31 95.6% 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 Mon Oct 10 2011 at 14:25:20 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3060 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.157896 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): -15.74700 36.44500 ymin,ymax (A): -13.36200 60.87700 zmin,zma (A): 19.09600 76.69901 x,y,z range (A): 52.19200 74.23900 57.60300 scale (grids/A): 2.157896 object centre (A): 10.34900 23.75750 47.89750 number of atom coordinates read : 3060 total number of charged atoms : 2911 net assigned charge : -0.4999888 assigned positive charge : 457.2702 centred at (gu) : 90.39966 94.19595 98.65250 assigned negative charge : -457.7713 centred at (gu) : 90.09113 94.56377 98.52479 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 118766 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31572 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 46128 mr = 77973 m= 9776 mr = 33114 m= 1049 mr = 6181 m= 34 mr = 491 m= 3 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 809 time to turn everything in is 0.8500000 number of dielectric boundary points 57994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 75 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 23160 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) : 1.438597 object centre at (A) : 10.34900 23.75750 47.89750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4162663E-02 3.1615924E-02 midg,1,midg; midg,igrid,midg 3.9388940E-02 -0.2124985 1,midg,midg; igrid,midg,midg -2.8768487E-02 8.0543838E-02 gauss-seidel spectral radius is 0.9989690 estimated iterations to convergence 246 setup time was (sec) 1.110000 now iterating at: 14:25:22 rms-change max change #iterations 7.198181 260.7673 at 10iterations 3.860692 115.2796 at 20iterations 2.051901 64.14906 at 30iterations 1.086116 31.28073 at 40iterations 0.5720357 20.42914 at 50iterations 0.2997828 7.212315 at 60iterations 0.1566803 4.057793 at 70iterations 8.1974238E-02 2.235168 at 80iterations 4.2675674E-02 1.117596 at 90iterations 2.2290625E-02 0.5746045 at 100iterations 1.1599614E-02 0.2979640 at 110iterations 6.0211895E-03 0.1443963 at 120iterations 3.1340881E-03 7.5052261E-02 at 130iterations 1.6267617E-03 4.6623230E-02 at 140iterations 8.4451138E-04 1.9893646E-02 at 150iterations 4.3853704E-04 1.2125969E-02 at 160iterations 2.2759775E-04 5.5465698E-03 at 170iterations 1.1816924E-04 2.7875900E-03 at 180iterations finished qdiffx linear iterations at : 14:25:31 total time elapsed so far: 10.33000 # loops : 180 mean,max change (kT/e) : 1.1816924E-04 2.7875900E-03 energy calculations done at 10.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.50000 DelPhi exited at 14:25:31 10.498u 0.193s 0:11.00 97.0% 0+0k 0+0io 0pf+0w