Sat Oct 8 22:10:19 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 Sat Oct 8 2011 at 22:10:19 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 = 2328 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: 0.5742769 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): -13.99600 40.94700 ymin,ymax (A): -31.63500 30.35600 zmin,zma (A): -8.730000 32.43300 x,y,z range (A): 54.94300 61.99100 41.16300 scale (grids/A): 0.5742769 object centre (A): 13.47550 -0.6395006 11.85150 number of atom coordinates read : 2328 total number of charged atoms : 2193 net assigned charge : 11.00002 assigned positive charge : 336.8105 centred at (gu) : 89.54915 90.24512 91.23502 assigned negative charge : -325.8112 centred at (gu) : 89.59675 90.29610 91.15132 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5281 nv = 96 ne = 84 npr = 44898 no. pairs analyzed = 44898 no. exposed pairs = 3160 no. arc points = 22866 no. surface atoms = 1060 nbur = 1268 mkacc time = 9.9999994E-02 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 = 1.512000 m= 251 mr = 2610 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2298 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6551 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3316463E-10 4.0750474E-09 midg,1,midg; midg,igrid,midg 2.4765670E-09 1.3351426E-09 1,midg,midg; igrid,midg,midg 2.8610945E-09 1.1848345E-09 gauss-seidel spectral radius is 0.9843112 estimated iterations to convergence 66 setup time was (sec) 0.5000000 now iterating at: 22:10:20 rms-change max change #iterations 7.9943784E-02 13.51905 at 10iterations 6.1264569E-03 1.095769 at 20iterations 5.2250194E-04 8.9233398E-02 at 30iterations 7.1375725E-05 1.3738632E-02 at 40iterations 1.4653881E-05 3.1127930E-03 at 50iterations finished qdiffx linear iterations at : 22:10:22 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 1.4653881E-05 3.1127930E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 22:10:23 3.151u 0.175s 0:03.65 90.9% 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 Sat Oct 8 2011 at 22:10:23 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 = 2328 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: 1.722831 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): -13.99600 40.94700 ymin,ymax (A): -31.63500 30.35600 zmin,zma (A): -8.730000 32.43300 x,y,z range (A): 54.94300 61.99100 41.16300 scale (grids/A): 1.722831 object centre (A): 13.47550 -0.6395006 11.85150 number of atom coordinates read : 2328 total number of charged atoms : 2193 net assigned charge : 11.00002 assigned positive charge : 336.8105 centred at (gu) : 88.64741 90.73486 93.70465 assigned negative charge : -325.8112 centred at (gu) : 88.79023 90.88839 93.45406 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 57000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22866 grid for indexing accessible points = 1.400000 m= 19111 mr = 36944 m= 2523 mr = 13209 m= 102 mr = 1274 m= 0 mr = 11 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 27298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 223 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 16999 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) : 0.5742769 object centre at (A) : 13.47550 -0.6395006 11.85150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6151582E-03 1.4270059E-02 midg,1,midg; midg,igrid,midg 3.2745209E-02 1.3780190E-02 1,midg,midg; igrid,midg,midg 2.2763288E-02 1.2916009E-02 gauss-seidel spectral radius is 0.9983238 estimated iterations to convergence 194 setup time was (sec) 0.7000000 now iterating at: 22:10:24 rms-change max change #iterations 3.130126 195.7099 at 10iterations 1.353268 67.71887 at 20iterations 0.5788954 21.05897 at 30iterations 0.2482532 9.928415 at 40iterations 0.1067923 3.902565 at 50iterations 4.6008386E-02 1.766487 at 60iterations 1.9792568E-02 0.7861814 at 70iterations 8.5537946E-03 0.3005295 at 80iterations 3.6799223E-03 0.1317139 at 90iterations 1.5897672E-03 6.2540054E-02 at 100iterations 6.8836188E-04 2.6710510E-02 at 110iterations 3.0057330E-04 1.1888504E-02 at 120iterations finished qdiffx linear iterations at : 22:10:30 total time elapsed so far: 7.180000 # loops : 120 mean,max change (kT/e) : 3.0057330E-04 1.1888504E-02 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.360000 DelPhi exited at 22:10:31 7.364u 0.205s 0:07.85 96.3% 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 Sat Oct 8 2011 at 22:10:31 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 = 2328 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: 2.584246 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): -13.99600 40.94700 ymin,ymax (A): -31.63500 30.35600 zmin,zma (A): -8.730000 32.43300 x,y,z range (A): 54.94300 61.99100 41.16300 scale (grids/A): 2.584246 object centre (A): 13.47550 -0.6395006 11.85150 number of atom coordinates read : 2328 total number of charged atoms : 2193 net assigned charge : 11.00002 assigned positive charge : 336.8105 centred at (gu) : 87.97115 91.10236 95.55705 assigned negative charge : -325.8112 centred at (gu) : 88.18547 91.33264 95.18114 start vw surface at 0.1400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 132094 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22866 grid for indexing accessible points = 1.400000 m= 63073 mr = 90790 m= 20817 mr = 49524 m= 4160 mr = 15754 m= 427 mr = 2709 m= 10 mr = 194 m= 0 mr = 4 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.010000 number of dielectric boundary points 61606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 17534 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) : 1.722831 object centre at (A) : 13.47550 -0.6395006 11.85150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1058574E-02 0.1839206 midg,1,midg; midg,igrid,midg 0.5046034 0.3113166 1,midg,midg; igrid,midg,midg 0.2884710 0.2004727 gauss-seidel spectral radius is 0.9991740 estimated iterations to convergence 275 setup time was (sec) 1.320000 now iterating at: 22:10:32 rms-change max change #iterations 7.973502 322.1510 at 10iterations 4.562724 132.3922 at 20iterations 2.588335 62.81869 at 30iterations 1.458962 36.55660 at 40iterations 0.8239653 21.40026 at 50iterations 0.4615943 11.41603 at 60iterations 0.2585767 5.659088 at 70iterations 0.1444878 3.109700 at 80iterations 8.0650315E-02 1.884662 at 90iterations 4.5021463E-02 0.9976692 at 100iterations 2.5124487E-02 0.5120938 at 110iterations 1.3993612E-02 0.3214626 at 120iterations 7.7660275E-03 0.1770511 at 130iterations 4.3336172E-03 8.7394714E-02 at 140iterations 2.4094975E-03 5.1270485E-02 at 150iterations 1.3378769E-03 3.2492638E-02 at 160iterations 7.4347039E-04 1.5713692E-02 at 170iterations 4.1407911E-04 9.2315674E-03 at 180iterations finished qdiffx linear iterations at : 22:10:43 total time elapsed so far: 11.56000 # loops : 180 mean,max change (kT/e) : 4.1407911E-04 9.2315674E-03 energy calculations done at 11.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.73000 DelPhi exited at 22:10:43 11.729u 0.204s 0:12.21 97.6% 0+0k 0+0io 0pf+0w