Wed Dec 28 11:06:36 PST 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 Wed Dec 28 2011 at 11:06:36 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 = 1964 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: 0.6534148 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): -5.651000 34.30600 ymin,ymax (A): -3.454000 49.28300 zmin,zma (A): -23.69700 30.78600 x,y,z range (A): 39.95700 52.73700 54.48300 scale (grids/A): 0.6534148 object centre (A): 14.32750 22.91450 3.544500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 90.70384 92.35694 90.07565 assigned negative charge : -285.8263 centred at (gu) : 90.82968 92.49787 89.99157 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5682 nv = 96 ne = 84 npr = 40586 no. pairs analyzed = 40586 no. exposed pairs = 2483 no. arc points = 17625 no. surface atoms = 846 nbur = 1118 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 303 mr = 3154 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3500000 number of dielectric boundary points 2798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1765 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 6716 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4374110E-09 1.5220404E-08 midg,1,midg; midg,igrid,midg 1.3294875E-08 -2.1303604E-08 1,midg,midg; igrid,midg,midg 1.7207777E-08 -1.2537470E-08 gauss-seidel spectral radius is 0.9878058 estimated iterations to convergence 74 setup time was (sec) 0.7600000 now iterating at: 11:06:37 rms-change max change #iterations 0.1335798 21.29362 at 10iterations 1.3731716E-02 2.128217 at 20iterations 1.4165641E-03 0.2522926 at 30iterations 1.4613544E-04 2.4158478E-02 at 40iterations 1.5097237E-05 2.4350882E-03 at 50iterations finished qdiffx linear iterations at : 11:06:43 total time elapsed so far: 6.300000 # loops : 50 mean,max change (kT/e) : 1.5097237E-05 2.4350882E-03 energy calculations done at 6.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.510000 DelPhi exited at 11:06:43 6.513u 0.605s 0:07.53 94.4% 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 Wed Dec 28 2011 at 11:06:43 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 = 1964 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: 1.960244 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): -5.651000 34.30600 ymin,ymax (A): -3.454000 49.28300 zmin,zma (A): -23.69700 30.78600 x,y,z range (A): 39.95700 52.73700 54.48300 scale (grids/A): 1.960244 object centre (A): 14.32750 22.91450 3.544500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 92.11160 97.07073 90.22697 assigned negative charge : -285.8263 centred at (gu) : 92.48921 97.49380 89.97484 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 61079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17625 grid for indexing accessible points = 1.400000 m= 22070 mr = 41814 m= 3299 mr = 16688 m= 142 mr = 2143 m= 0 mr = 62 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 2509 time to turn everything in is 0.7100000 number of dielectric boundary points 25883 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 14456 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) : 0.6534148 object centre at (A) : 14.32750 22.91450 3.544500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8631037E-02 1.5537078E-02 midg,1,midg; midg,igrid,midg 3.5013363E-02 -2.1896249E-02 1,midg,midg; igrid,midg,midg 6.5756072E-03 -7.0758094E-03 gauss-seidel spectral radius is 0.9986336 estimated iterations to convergence 214 setup time was (sec) 1.180000 now iterating at: 11:06:45 rms-change max change #iterations 3.735960 185.0824 at 10iterations 1.754449 70.13831 at 20iterations 0.8222604 32.25808 at 30iterations 0.3841932 13.96484 at 40iterations 0.1795363 6.603265 at 50iterations 8.4104121E-02 2.796177 at 60iterations 3.9157752E-02 1.343693 at 70iterations 1.8382402E-02 0.5881123 at 80iterations 8.5638911E-03 0.2750931 at 90iterations 4.0095877E-03 0.1634750 at 100iterations 1.8837848E-03 6.3297272E-02 at 110iterations 8.8108884E-04 3.3683777E-02 at 120iterations finished qdiffx linear iterations at : 11:07:01 total time elapsed so far: 16.95000 # loops : 120 mean,max change (kT/e) : 8.8108884E-04 3.3683777E-02 energy calculations done at 16.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.17000 DelPhi exited at 11:07:02 17.174u 0.709s 0:18.18 98.2% 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 Wed Dec 28 2011 at 11:07:02 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 = 1964 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: 2.940367 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): -5.651000 34.30600 ymin,ymax (A): -3.454000 49.28300 zmin,zma (A): -23.69700 30.78600 x,y,z range (A): 39.95700 52.73700 54.48300 scale (grids/A): 2.940367 object centre (A): 14.32750 22.91450 3.544500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 93.16743 100.6061 90.34050 assigned negative charge : -285.8263 centred at (gu) : 93.73370 101.2408 89.96221 start vw surface at 0.1300000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 141309 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17625 grid for indexing accessible points = 1.400000 m= 71285 mr = 101285 m= 25601 mr = 58831 m= 5768 mr = 21189 m= 720 mr = 4493 m= 38 mr = 520 m= 0 mr = 17 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 8444 time to turn everything in is 1.790000 number of dielectric boundary points 58386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 14656 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) : 1.960244 object centre at (A) : 14.32750 22.91450 3.544500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8670978 4.4046361E-02 midg,1,midg; midg,igrid,midg 0.3374673 -0.2487373 1,midg,midg; igrid,midg,midg 3.5123147E-02 -4.3260649E-02 gauss-seidel spectral radius is 0.9992465 estimated iterations to convergence 288 setup time was (sec) 2.310000 now iterating at: 11:07:05 rms-change max change #iterations 8.728181 386.3246 at 10iterations 5.015903 132.2074 at 20iterations 2.862976 62.17827 at 30iterations 1.634273 31.59770 at 40iterations 0.9341441 17.94296 at 50iterations 0.5329654 10.55305 at 60iterations 0.3029552 6.281281 at 70iterations 0.1732170 3.543285 at 80iterations 9.8443083E-02 2.011900 at 90iterations 5.6099117E-02 1.058678 at 100iterations 3.2049544E-02 0.6248245 at 110iterations 1.8347943E-02 0.3426971 at 120iterations 1.0422553E-02 0.2003661 at 130iterations 5.9379181E-03 0.1144571 at 140iterations 3.3945495E-03 6.8548858E-02 at 150iterations 1.9314580E-03 3.8333893E-02 at 160iterations 1.1015091E-03 2.0435333E-02 at 170iterations 6.2856160E-04 1.2845993E-02 at 180iterations finished qdiffx linear iterations at : 11:07:33 total time elapsed so far: 30.32000 # loops : 180 mean,max change (kT/e) : 6.2856160E-04 1.2845993E-02 energy calculations done at 30.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.54000 DelPhi exited at 11:07:33 30.541u 0.810s 0:31.74 98.7% 0+0k 0+0io 0pf+0w