Sun Oct 9 10:34:57 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 Sun Oct 9 2011 at 10:34:57 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2926 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: CME 218 has a net charge of -0.3480 !!! WARNING: CME 314 has a net charge of -0.3480 !!! WARNING: CME 463 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 0.5826991 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): -17.90100 43.19400 ymin,ymax (A): -27.79600 25.50800 zmin,zma (A): -29.17000 27.26700 x,y,z range (A): 61.09500 53.30400 56.43700 scale (grids/A): 0.5826991 object centre (A): 12.64650 -1.143999 -0.9514999 number of atom coordinates read : 2926 total number of charged atoms : 2830 net assigned charge : 1.333027 assigned positive charge : 437.3199 centred at (gu) : 88.37046 90.82784 91.78244 assigned negative charge : -435.9887 centred at (gu) : 88.34686 90.77145 91.72352 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6934 nv = 96 ne = 84 npr = 55986 no. pairs analyzed = 55986 no. exposed pairs = 4142 no. arc points = 29024 no. surface atoms = 1376 nbur = 1550 mkacc time = 0.1300000 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 = 1.484000 m= 352 mr = 3437 m= 0 mr = 30 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2869 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8622 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2063444E-10 2.5343319E-09 midg,1,midg; midg,igrid,midg -8.5410640E-10 1.9459658E-09 1,midg,midg; igrid,midg,midg -4.0299022E-10 5.7660476E-10 gauss-seidel spectral radius is 0.9848075 estimated iterations to convergence 67 setup time was (sec) 0.6200000 now iterating at: 10:34:58 rms-change max change #iterations 0.1015236 14.84294 at 10iterations 8.0626970E-03 1.285373 at 20iterations 7.8934804E-04 0.1175671 at 30iterations 1.5041862E-04 2.3500443E-02 at 40iterations 4.1330557E-05 6.3738823E-03 at 50iterations finished qdiffx linear iterations at : 10:35:01 total time elapsed so far: 4.520000 # loops : 50 mean,max change (kT/e) : 4.1330557E-05 6.3738823E-03 energy calculations done at 4.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.690000 DelPhi exited at 10:35:02 4.698u 0.286s 0:05.26 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 Sun Oct 9 2011 at 10:35:02 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2926 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: CME 218 has a net charge of -0.3480 !!! WARNING: CME 314 has a net charge of -0.3480 !!! WARNING: CME 463 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 1.748097 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): -17.90100 43.19400 ymin,ymax (A): -27.79600 25.50800 zmin,zma (A): -29.17000 27.26700 x,y,z range (A): 61.09500 53.30400 56.43700 scale (grids/A): 1.748097 object centre (A): 12.64650 -1.143999 -0.9514999 number of atom coordinates read : 2926 total number of charged atoms : 2830 net assigned charge : 1.333027 assigned positive charge : 437.3199 centred at (gu) : 85.11075 92.48270 95.34608 assigned negative charge : -435.9887 centred at (gu) : 85.04044 92.31425 95.17066 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75809 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29024 grid for indexing accessible points = 1.400000 m= 25547 mr = 50747 m= 3480 mr = 17112 m= 129 mr = 1729 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 35356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 21982 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) : 0.5826991 object centre at (A) : 12.64650 -1.143999 -0.9514999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3779174E-02 8.9836391E-03 midg,1,midg; midg,igrid,midg 9.8331114E-03 7.9896711E-03 1,midg,midg; igrid,midg,midg 2.1223017E-04 1.9433725E-03 gauss-seidel spectral radius is 0.9984396 estimated iterations to convergence 201 setup time was (sec) 0.9700000 now iterating at: 10:35:03 rms-change max change #iterations 3.812490 182.0262 at 10iterations 1.679717 55.72168 at 20iterations 0.7439243 25.27687 at 30iterations 0.3295043 10.64516 at 40iterations 0.1462817 5.231747 at 50iterations 6.4954519E-02 2.342247 at 60iterations 2.8954087E-02 0.9681969 at 70iterations 1.2862504E-02 0.4103184 at 80iterations 5.7449718E-03 0.1844978 at 90iterations 2.5801468E-03 9.1903687E-02 at 100iterations 1.1769945E-03 3.7830353E-02 at 110iterations 5.4459536E-04 1.9525528E-02 at 120iterations finished qdiffx linear iterations at : 10:35:12 total time elapsed so far: 10.05000 # loops : 120 mean,max change (kT/e) : 5.4459536E-04 1.9525528E-02 energy calculations done at 10.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.23000 DelPhi exited at 10:35:13 10.234u 0.360s 0:11.02 96.0% 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 10:35:13 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2926 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: CME 218 has a net charge of -0.3480 !!! WARNING: CME 314 has a net charge of -0.3480 !!! WARNING: CME 463 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 2.622146 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): -17.90100 43.19400 ymin,ymax (A): -27.79600 25.50800 zmin,zma (A): -29.17000 27.26700 x,y,z range (A): 61.09500 53.30400 56.43700 scale (grids/A): 2.622146 object centre (A): 12.64650 -1.143999 -0.9514999 number of atom coordinates read : 2926 total number of charged atoms : 2830 net assigned charge : 1.333027 assigned positive charge : 437.3199 centred at (gu) : 82.66587 93.72395 98.01893 assigned negative charge : -435.9887 centred at (gu) : 82.56072 93.47137 97.75585 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 175603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29024 grid for indexing accessible points = 1.400000 m= 84534 mr = 124581 m= 27703 mr = 65501 m= 5790 mr = 20346 m= 549 mr = 3758 m= 17 mr = 239 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.590000 number of dielectric boundary points 79772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 22628 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) : 1.748097 object centre at (A) : 12.64650 -1.143999 -0.9514999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1874049 8.7654106E-02 midg,1,midg; midg,igrid,midg 0.2251774 8.6023271E-02 1,midg,midg; igrid,midg,midg -5.0013126E-03 9.5519885E-02 gauss-seidel spectral radius is 0.9992189 estimated iterations to convergence 282 setup time was (sec) 1.960000 now iterating at: 10:35:15 rms-change max change #iterations 9.601912 277.2323 at 10iterations 5.631008 172.2344 at 20iterations 3.276291 75.36282 at 30iterations 1.893760 41.02619 at 40iterations 1.087963 21.04288 at 50iterations 0.6242546 12.05412 at 60iterations 0.3568597 8.691849 at 70iterations 0.2040157 4.282162 at 80iterations 0.1161418 2.120428 at 90iterations 6.5973312E-02 1.221596 at 100iterations 3.7589855E-02 0.7190733 at 110iterations 2.1356996E-02 0.4076748 at 120iterations 1.2172389E-02 0.2444115 at 130iterations 6.9362046E-03 0.1376686 at 140iterations 3.9618732E-03 7.5103760E-02 at 150iterations 2.2736129E-03 4.5165539E-02 at 160iterations 1.3229420E-03 2.9264450E-02 at 170iterations 7.8562379E-04 1.6925812E-02 at 180iterations finished qdiffx linear iterations at : 10:35:29 total time elapsed so far: 15.62000 # loops : 180 mean,max change (kT/e) : 7.8562379E-04 1.6925812E-02 energy calculations done at 15.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.81000 DelPhi exited at 10:35:30 15.812u 0.310s 0:16.57 97.2% 0+0k 0+0io 0pf+0w