Tue Oct 11 08:39:06 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 08:39:06 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 = 2049 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: 0.7092764 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): -5.226000 44.96600 ymin,ymax (A): 38.75000 85.47100 zmin,zma (A): -13.53200 28.37800 x,y,z range (A): 50.19200 46.72100 41.91000 scale (grids/A): 0.7092764 object centre (A): 19.87000 62.11050 7.423000 number of atom coordinates read : 2049 total number of charged atoms : 1921 net assigned charge : 6.500009 assigned positive charge : 310.1990 centred at (gu) : 90.94501 90.97959 90.34216 assigned negative charge : -303.6992 centred at (gu) : 90.88417 90.88372 90.40398 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6921 nv = 96 ne = 84 npr = 41280 no. pairs analyzed = 41280 no. exposed pairs = 2466 no. arc points = 16862 no. surface atoms = 841 nbur = 1208 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 475 mr = 4008 m= 5 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1599 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7760 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1726270E-08 2.6876648E-08 midg,1,midg; midg,igrid,midg 7.1525483E-09 1.2579319E-07 1,midg,midg; igrid,midg,midg 2.1951349E-08 1.0408249E-07 gauss-seidel spectral radius is 0.9896339 estimated iterations to convergence 80 setup time was (sec) 0.3500000 now iterating at: 08:39:06 rms-change max change #iterations 0.1981571 28.17773 at 10iterations 2.4546515E-02 3.067944 at 20iterations 3.2753076E-03 0.4123764 at 30iterations 5.0801045E-04 6.2107086E-02 at 40iterations 1.1858682E-04 1.5506744E-02 at 50iterations finished qdiffx linear iterations at : 08:39:09 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.1858682E-04 1.5506744E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 08:39:10 3.410u 0.182s 0:04.07 88.2% 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 08:39:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2049 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: 2.127829 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): -5.226000 44.96600 ymin,ymax (A): 38.75000 85.47100 zmin,zma (A): -13.53200 28.37800 x,y,z range (A): 50.19200 46.72100 41.91000 scale (grids/A): 2.127829 object centre (A): 19.87000 62.11050 7.423000 number of atom coordinates read : 2049 total number of charged atoms : 1921 net assigned charge : 6.500009 assigned positive charge : 310.1990 centred at (gu) : 92.83503 92.93909 91.02663 assigned negative charge : -303.6992 centred at (gu) : 92.65276 92.65140 91.21198 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74188 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16862 grid for indexing accessible points = 1.400000 m= 29441 mr = 52964 m= 5459 mr = 22226 m= 465 mr = 3555 m= 18 mr = 251 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 30575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 15254 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) : 0.7092764 object centre at (A) : 19.87000 62.11050 7.423000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6330983E-02 2.5838664E-02 midg,1,midg; midg,igrid,midg -4.6442404E-02 3.2806743E-02 1,midg,midg; igrid,midg,midg 6.2354803E-02 4.8533384E-02 gauss-seidel spectral radius is 0.9988322 estimated iterations to convergence 232 setup time was (sec) 0.6100000 now iterating at: 08:39:11 rms-change max change #iterations 4.561410 187.8156 at 10iterations 2.258484 72.83034 at 20iterations 1.121404 35.71028 at 30iterations 0.5570954 16.62372 at 40iterations 0.2752228 8.136946 at 50iterations 0.1369948 4.321253 at 60iterations 6.8355083E-02 2.171455 at 70iterations 3.3925239E-02 0.9873276 at 80iterations 1.6952038E-02 0.5062972 at 90iterations 8.4805982E-03 0.2516556 at 100iterations 4.2569563E-03 0.1316738 at 110iterations 2.1676426E-03 6.8845749E-02 at 120iterations finished qdiffx linear iterations at : 08:39:18 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 2.1676426E-03 6.8845749E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 08:39:19 7.919u 0.195s 0:08.56 94.6% 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 Tue Oct 11 2011 at 08:39:19 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 = 2049 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: 3.191744 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): -5.226000 44.96600 ymin,ymax (A): 38.75000 85.47100 zmin,zma (A): -13.53200 28.37800 x,y,z range (A): 50.19200 46.72100 41.91000 scale (grids/A): 3.191744 object centre (A): 19.87000 62.11050 7.423000 number of atom coordinates read : 2049 total number of charged atoms : 1921 net assigned charge : 6.500009 assigned positive charge : 310.1990 centred at (gu) : 94.25259 94.40870 91.53992 assigned negative charge : -303.6992 centred at (gu) : 93.97914 93.97701 91.81807 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 171356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16862 grid for indexing accessible points = 1.400000 m= 92447 mr = 127694 m= 36965 mr = 76955 m= 10190 mr = 30147 m= 1973 mr = 7861 m= 266 mr = 1412 m= 7 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.130000 number of dielectric boundary points 68970 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 15368 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) : 2.127829 object centre at (A) : 19.87000 62.11050 7.423000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5197948E-02 0.1884953 midg,1,midg; midg,igrid,midg -0.4992288 0.2753187 1,midg,midg; igrid,midg,midg 0.5094397 0.3666476 gauss-seidel spectral radius is 0.9992964 estimated iterations to convergence 297 setup time was (sec) 1.370000 now iterating at: 08:39:20 rms-change max change #iterations 10.13019 423.4858 at 10iterations 5.971621 128.5461 at 20iterations 3.516455 65.87115 at 30iterations 2.067497 46.10618 at 40iterations 1.212025 23.47019 at 50iterations 0.7118375 13.48127 at 60iterations 0.4182019 8.222794 at 70iterations 0.2444369 4.540304 at 80iterations 0.1431306 2.719006 at 90iterations 8.3920509E-02 1.854139 at 100iterations 4.9275029E-02 0.9875069 at 110iterations 2.8943649E-02 0.4870949 at 120iterations 1.7074218E-02 0.3275032 at 130iterations 1.0192424E-02 0.1774101 at 140iterations 6.2022186E-03 0.1212349 at 150iterations 3.8624250E-03 7.4413300E-02 at 160iterations 2.5359043E-03 4.8971176E-02 at 170iterations 1.7496448E-03 3.5217285E-02 at 180iterations finished qdiffx linear iterations at : 08:39:31 total time elapsed so far: 12.45000 # loops : 180 mean,max change (kT/e) : 1.7496448E-03 3.5217285E-02 energy calculations done at 12.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 08:39:32 12.582u 0.199s 0:13.21 96.6% 0+0k 0+0io 0pf+0w