Sat Oct 8 20:40:51 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 Sat Oct 8 2011 at 20:40:51 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 472 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: 0.6261322 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): -31.90500 17.46400 ymin,ymax (A): -24.11400 22.84500 zmin,zma (A): -12.00900 44.84800 x,y,z range (A): 49.36900 46.95900 56.85700 scale (grids/A): 0.6261322 object centre (A): -7.220500 -0.6345005 16.41950 number of atom coordinates read : 2573 total number of charged atoms : 2457 net assigned charge : 4.000010 assigned positive charge : 393.5971 centred at (gu) : 88.55277 89.43148 89.58215 assigned negative charge : -389.5976 centred at (gu) : 88.46890 89.47385 89.48448 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6656 nv = 96 ne = 84 npr = 53180 no. pairs analyzed = 53180 no. exposed pairs = 2980 no. arc points = 21360 no. surface atoms = 1004 nbur = 1569 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 322 mr = 3754 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 106 time to turn everything in is 0.3500000 number of dielectric boundary points 3180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2142 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8223 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2348089E-09 1.0649527E-08 midg,1,midg; midg,igrid,midg 8.3101828E-09 5.6862837E-10 1,midg,midg; igrid,midg,midg -3.8601793E-09 7.7454461E-09 gauss-seidel spectral radius is 0.9867834 estimated iterations to convergence 71 setup time was (sec) 0.6200000 now iterating at: 20:40:52 rms-change max change #iterations 0.1334035 19.27844 at 10iterations 1.2286205E-02 1.734470 at 20iterations 1.1722496E-03 0.1679764 at 30iterations 1.1075537E-04 1.6582489E-02 at 40iterations 1.0567083E-05 1.4629364E-03 at 50iterations finished qdiffx linear iterations at : 20:40:55 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 1.0567083E-05 1.4629364E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 20:40:55 4.087u 0.246s 0:04.60 93.9% 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 20:40:55 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 472 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: 1.878397 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): -31.90500 17.46400 ymin,ymax (A): -24.11400 22.84500 zmin,zma (A): -12.00900 44.84800 x,y,z range (A): 49.36900 46.95900 56.85700 scale (grids/A): 1.878397 object centre (A): -7.220500 -0.6345005 16.41950 number of atom coordinates read : 2573 total number of charged atoms : 2457 net assigned charge : 4.000010 assigned positive charge : 393.5971 centred at (gu) : 85.65813 88.29408 88.74576 assigned negative charge : -389.5976 centred at (gu) : 85.40664 88.42136 88.45338 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 72193 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21360 grid for indexing accessible points = 1.400000 m= 25909 mr = 50690 m= 3940 mr = 19474 m= 239 mr = 2540 m= 0 mr = 93 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 3011 time to turn everything in is 0.6400000 number of dielectric boundary points 29484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19265 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) : 0.6261322 object centre at (A) : -7.220500 -0.6345005 16.41950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1654585E-02 1.8532790E-02 midg,1,midg; midg,igrid,midg 1.4592372E-02 3.4986888E-03 1,midg,midg; igrid,midg,midg -2.4088568E-03 2.9936224E-02 gauss-seidel spectral radius is 0.9985934 estimated iterations to convergence 211 setup time was (sec) 0.9400000 now iterating at: 20:40:57 rms-change max change #iterations 4.119294 164.4440 at 10iterations 1.904102 69.68542 at 20iterations 0.8823373 28.93506 at 30iterations 0.4078094 14.12012 at 40iterations 0.1894286 6.207939 at 50iterations 8.7626740E-02 2.760170 at 60iterations 4.0606029E-02 1.270918 at 70iterations 1.8849090E-02 0.5746331 at 80iterations 8.7228678E-03 0.2738018 at 90iterations 4.0341006E-03 0.1302567 at 100iterations 1.8696436E-03 6.6256523E-02 at 110iterations 8.6633331E-04 2.5886536E-02 at 120iterations finished qdiffx linear iterations at : 20:41:05 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 8.6633331E-04 2.5886536E-02 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.390000 DelPhi exited at 20:41:05 9.391u 0.290s 0:09.95 97.2% 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 Sat Oct 8 2011 at 20:41:05 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 472 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: 2.817595 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): -31.90500 17.46400 ymin,ymax (A): -24.11400 22.84500 zmin,zma (A): -12.00900 44.84800 x,y,z range (A): 49.36900 46.95900 56.85700 scale (grids/A): 2.817595 object centre (A): -7.220500 -0.6345005 16.41950 number of atom coordinates read : 2573 total number of charged atoms : 2457 net assigned charge : 4.000010 assigned positive charge : 393.5971 centred at (gu) : 83.48726 87.44112 88.11850 assigned negative charge : -389.5976 centred at (gu) : 83.11003 87.63211 87.68007 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 167020 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21360 grid for indexing accessible points = 1.400000 m= 85008 mr = 122421 m= 29905 mr = 70506 m= 7094 mr = 24389 m= 965 mr = 5449 m= 43 mr = 683 m= 0 mr = 13 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 10528 time to turn everything in is 1.630000 number of dielectric boundary points 66574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 19651 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) : 1.878397 object centre at (A) : -7.220500 -0.6345005 16.41950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2517221 0.2225761 midg,1,midg; midg,igrid,midg 0.1808981 3.8987294E-02 1,midg,midg; igrid,midg,midg -2.9268937E-02 0.3968872 gauss-seidel spectral radius is 0.9992427 estimated iterations to convergence 287 setup time was (sec) 1.940000 now iterating at: 20:41:08 rms-change max change #iterations 9.635209 393.7980 at 10iterations 5.536987 111.9134 at 20iterations 3.164088 58.77032 at 30iterations 1.807874 34.20991 at 40iterations 1.031454 20.14121 at 50iterations 0.5867352 10.28160 at 60iterations 0.3355598 5.849739 at 70iterations 0.1916339 3.638592 at 80iterations 0.1090109 1.928543 at 90iterations 6.2104870E-02 1.096302 at 100iterations 3.5426065E-02 0.6730652 at 110iterations 2.0157751E-02 0.3608093 at 120iterations 1.1517733E-02 0.2043457 at 130iterations 6.5719541E-03 0.1263790 at 140iterations 3.7305560E-03 6.6775322E-02 at 150iterations 2.1354568E-03 4.2236328E-02 at 160iterations 1.2144487E-03 2.1785736E-02 at 170iterations 6.9274451E-04 1.3015747E-02 at 180iterations finished qdiffx linear iterations at : 20:41:21 total time elapsed so far: 15.46000 # loops : 180 mean,max change (kT/e) : 6.9274451E-04 1.3015747E-02 energy calculations done at 15.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.64000 DelPhi exited at 20:41:22 15.646u 0.309s 0:16.22 98.2% 0+0k 0+0io 0pf+0w