Mon Oct 10 09:14:52 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 09:14:53 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: 0.6536428 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): -4.194000 34.45500 ymin,ymax (A): -3.431000 47.88600 zmin,zma (A): -23.66300 30.80100 x,y,z range (A): 38.64900 51.31700 54.46400 scale (grids/A): 0.6536428 object centre (A): 15.13050 22.22750 3.569000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.28439 92.61933 90.05978 assigned negative charge : -284.8263 centred at (gu) : 90.39420 92.75263 90.00049 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5606 nv = 96 ne = 84 npr = 40849 no. pairs analyzed = 40849 no. exposed pairs = 2463 no. arc points = 17364 no. surface atoms = 831 nbur = 1133 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 326 mr = 3070 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.2600000 number of dielectric boundary points 2824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1729 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6663 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7519510E-10 1.4277160E-08 midg,1,midg; midg,igrid,midg 1.3331837E-08 -1.7372708E-08 1,midg,midg; igrid,midg,midg 1.8990187E-08 -7.1098478E-09 gauss-seidel spectral radius is 0.9878126 estimated iterations to convergence 74 setup time was (sec) 0.4900000 now iterating at: 09:14:53 rms-change max change #iterations 0.1339335 19.94626 at 10iterations 1.4018689E-02 2.136042 at 20iterations 1.4512886E-03 0.2214203 at 30iterations 1.5066462E-04 2.4757385E-02 at 40iterations 1.5370284E-05 2.3412704E-03 at 50iterations finished qdiffx linear iterations at : 09:14:56 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.5370284E-05 2.3412704E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 09:14:56 3.385u 0.152s 0:03.83 92.1% 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 09:14:56 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: 1.960928 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): -4.194000 34.45500 ymin,ymax (A): -3.431000 47.88600 zmin,zma (A): -23.66300 30.80100 x,y,z range (A): 38.64900 51.31700 54.46400 scale (grids/A): 1.960928 object centre (A): 15.13050 22.22750 3.569000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.85297 97.85797 90.17984 assigned negative charge : -284.8263 centred at (gu) : 91.18282 98.25803 90.00152 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 60499 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17364 grid for indexing accessible points = 1.400000 m= 21935 mr = 41403 m= 3752 mr = 16594 m= 255 mr = 2501 m= 2 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1504 time to turn everything in is 0.4700000 number of dielectric boundary points 25859 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14469 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) : 0.6536428 object centre at (A) : 15.13050 22.22750 3.569000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2819401E-02 1.6119847E-02 midg,1,midg; midg,igrid,midg 4.6525411E-02 -4.8116720E-03 1,midg,midg; igrid,midg,midg 5.8413539E-03 -7.0185321E-03 gauss-seidel spectral radius is 0.9986311 estimated iterations to convergence 214 setup time was (sec) 0.7600000 now iterating at: 09:14:57 rms-change max change #iterations 3.771075 165.1864 at 10iterations 1.762628 64.16367 at 20iterations 0.8251131 30.29362 at 30iterations 0.3854448 13.31216 at 40iterations 0.1805844 6.130859 at 50iterations 8.3988719E-02 3.088727 at 60iterations 3.9476201E-02 1.368601 at 70iterations 1.8385259E-02 0.6686230 at 80iterations 8.6269863E-03 0.2831259 at 90iterations 4.0277373E-03 0.1344790 at 100iterations 1.8777464E-03 6.4864159E-02 at 110iterations 8.7792100E-04 2.8914928E-02 at 120iterations finished qdiffx linear iterations at : 09:15:04 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 8.7792100E-04 2.8914928E-02 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.340000 DelPhi exited at 09:15:04 7.347u 0.172s 0:07.79 96.4% 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 09:15:04 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.941392 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): -4.194000 34.45500 ymin,ymax (A): -3.431000 47.88600 zmin,zma (A): -23.66300 30.80100 x,y,z range (A): 38.64900 51.31700 54.46400 scale (grids/A): 2.941392 object centre (A): 15.13050 22.22750 3.569000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 91.27951 101.7869 90.26968 assigned negative charge : -284.8263 centred at (gu) : 91.77431 102.3871 90.00230 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 139629 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17364 grid for indexing accessible points = 1.400000 m= 70338 mr = 100296 m= 26503 mr = 57917 m= 6995 mr = 21897 m= 1117 mr = 5459 m= 50 mr = 758 m= 2 mr = 10 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 5294 time to turn everything in is 1.160000 number of dielectric boundary points 58298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 14652 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) : 1.960928 object centre at (A) : 15.13050 22.22750 3.569000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.169070 5.3686310E-02 midg,1,midg; midg,igrid,midg 0.5080202 -0.1190905 1,midg,midg; igrid,midg,midg 2.1669582E-02 -4.1688979E-02 gauss-seidel spectral radius is 0.9992448 estimated iterations to convergence 287 setup time was (sec) 1.450000 now iterating at: 09:15:06 rms-change max change #iterations 8.728730 332.4677 at 10iterations 5.002288 107.3641 at 20iterations 2.854599 57.48861 at 30iterations 1.632003 33.15807 at 40iterations 0.9329669 18.17989 at 50iterations 0.5306595 10.78267 at 60iterations 0.3026479 5.697758 at 70iterations 0.1726755 3.367312 at 80iterations 9.8449931E-02 1.857572 at 90iterations 5.6090400E-02 1.067780 at 100iterations 3.1923275E-02 0.5788994 at 110iterations 1.8201359E-02 0.3341064 at 120iterations 1.0347423E-02 0.2144375 at 130iterations 5.9084222E-03 0.1180267 at 140iterations 3.3656624E-03 6.2681198E-02 at 150iterations 1.9211207E-03 3.9115906E-02 at 160iterations 1.0949603E-03 1.9800663E-02 at 170iterations 6.2449637E-04 1.2180328E-02 at 180iterations finished qdiffx linear iterations at : 09:15:16 total time elapsed so far: 11.86000 # loops : 180 mean,max change (kT/e) : 6.2449637E-04 1.2180328E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.05000 DelPhi exited at 09:15:17 12.052u 0.180s 0:12.52 97.6% 0+0k 0+0io 0pf+0w