Sun Oct 9 02:57:39 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 Sun Oct 9 2011 at 02:57:39 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4563 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.4493985 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): -2.407000 76.81001 ymin,ymax (A): 0.8160001 67.06200 zmin,zma (A): 164.8370 225.3710 x,y,z range (A): 79.21700 66.24599 60.53398 scale (grids/A): 0.4493985 object centre (A): 37.20150 33.93900 195.1040 number of atom coordinates read : 4563 total number of charged atoms : 4329 net assigned charge : 19.00001 assigned positive charge : 668.4070 centred at (gu) : 85.94347 91.08031 88.96407 assigned negative charge : -649.4118 centred at (gu) : 85.89027 91.03022 88.98743 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5463 nv = 96 ne = 84 npr = 93677 no. pairs analyzed = 93677 no. exposed pairs = 5690 no. arc points = 39060 no. surface atoms = 1935 nbur = 2628 mkacc time = 0.1600000 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 = 1.876000 m= 142 mr = 2643 m= 0 mr = 2 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3100000 number of dielectric boundary points 2960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3347 ## 646 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7484 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0011276E-11 6.9297259E-12 midg,1,midg; midg,igrid,midg 4.5504416E-12 2.4569914E-11 1,midg,midg; igrid,midg,midg 1.8128273E-11 5.7071726E-12 gauss-seidel spectral radius is 0.9747151 estimated iterations to convergence 52 setup time was (sec) 0.4800000 now iterating at: 02:57:40 rms-change max change #iterations 3.4402058E-02 5.691406 at 10iterations 2.5890856E-03 0.4556274 at 20iterations 4.1807041E-04 6.6432953E-02 at 30iterations 7.6509466E-05 1.1882782E-02 at 40iterations 1.4135343E-05 2.1743774E-03 at 50iterations finished qdiffx linear iterations at : 02:57:43 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.4135343E-05 2.1743774E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 02:57:43 3.543u 0.161s 0:03.97 93.1% 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 Sun Oct 9 2011 at 02:57:43 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4563 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.348195 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): -2.407000 76.81001 ymin,ymax (A): 0.8160001 67.06200 zmin,zma (A): 164.8370 225.3710 x,y,z range (A): 79.21700 66.24599 60.53398 scale (grids/A): 1.348195 object centre (A): 37.20150 33.93900 195.1040 number of atom coordinates read : 4563 total number of charged atoms : 4329 net assigned charge : 19.00001 assigned positive charge : 668.4070 centred at (gu) : 77.82867 93.23930 86.89074 assigned negative charge : -649.4118 centred at (gu) : 77.67014 93.09042 86.96220 start vw surface at 0.1200000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 64156 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39060 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 15300 mr = 42866 m= 808 mr = 9281 m= 7 mr = 190 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 1170 time to turn everything in is 0.3400000 number of dielectric boundary points 27934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 609 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 30883 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) : 0.4493985 object centre at (A) : 37.20150 33.93900 195.1040 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0732073E-03 1.0490943E-03 midg,1,midg; midg,igrid,midg 2.4209099E-03 3.6939397E-03 1,midg,midg; igrid,midg,midg 2.4826301E-02 3.5839013E-03 gauss-seidel spectral radius is 0.9974318 estimated iterations to convergence 157 setup time was (sec) 0.5600000 now iterating at: 02:57:44 rms-change max change #iterations 2.641213 125.8011 at 10iterations 0.9279247 36.63686 at 20iterations 0.3304913 12.63670 at 30iterations 0.1168856 5.297056 at 40iterations 4.1807719E-02 1.751200 at 50iterations 1.4970989E-02 0.5827942 at 60iterations 5.5005993E-03 0.2180786 at 70iterations 2.1092677E-03 8.6402893E-02 at 80iterations 8.6516590E-04 3.4534454E-02 at 90iterations 3.8834516E-04 1.3402939E-02 at 100iterations 1.9137296E-04 6.6833496E-03 at 110iterations 9.9844881E-05 3.4112930E-03 at 120iterations finished qdiffx linear iterations at : 02:57:51 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 9.9844881E-05 3.4112930E-03 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 02:57:51 7.672u 0.178s 0:08.11 96.6% 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 Sun Oct 9 2011 at 02:57:51 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4563 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.022293 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): -2.407000 76.81001 ymin,ymax (A): 0.8160001 67.06200 zmin,zma (A): 164.8370 225.3710 x,y,z range (A): 79.21700 66.24599 60.53398 scale (grids/A): 2.022293 object centre (A): 37.20150 33.93900 195.1040 number of atom coordinates read : 4563 total number of charged atoms : 4329 net assigned charge : 19.00001 assigned positive charge : 668.4070 centred at (gu) : 71.74255 94.85870 85.33568 assigned negative charge : -649.4118 centred at (gu) : 71.50528 94.63551 85.44318 start vw surface at 0.1200000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 150108 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39060 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 58659 mr = 106285 m= 11410 mr = 43856 m= 1014 mr = 7458 m= 8 mr = 410 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 4032 time to turn everything in is 0.7600000 number of dielectric boundary points 63190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 34301 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) : 1.348195 object centre at (A) : 37.20150 33.93900 195.1040 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8506589E-02 1.5280409E-02 midg,1,midg; midg,igrid,midg 5.1154058E-02 7.6757781E-02 1,midg,midg; igrid,midg,midg 0.5841774 4.0793929E-02 gauss-seidel spectral radius is 0.9989156 estimated iterations to convergence 240 setup time was (sec) 0.9900000 now iterating at: 02:57:52 rms-change max change #iterations 7.784269 253.4632 at 10iterations 4.087128 108.6012 at 20iterations 2.140036 55.30528 at 30iterations 1.112887 25.87497 at 40iterations 0.5763706 13.15254 at 50iterations 0.2985404 6.932461 at 60iterations 0.1537560 3.577377 at 70iterations 7.8998230E-02 1.770166 at 80iterations 4.0646348E-02 0.9070473 at 90iterations 2.0875018E-02 0.4787979 at 100iterations 1.0725940E-02 0.2686415 at 110iterations 5.5286251E-03 0.1354713 at 120iterations 2.8500247E-03 6.7115784E-02 at 130iterations 1.4704922E-03 3.2055855E-02 at 140iterations 7.6222356E-04 1.7675400E-02 at 150iterations 4.0202009E-04 8.6289644E-03 at 160iterations 2.1451610E-04 4.9057007E-03 at 170iterations 1.1670151E-04 2.5100708E-03 at 180iterations finished qdiffx linear iterations at : 02:58:03 total time elapsed so far: 12.00000 # loops : 180 mean,max change (kT/e) : 1.1670151E-04 2.5100708E-03 energy calculations done at 12.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 02:58:04 12.127u 0.204s 0:12.59 97.8% 0+0k 0+0io 0pf+0w