Tue Oct 11 08:20:10 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 Tue Oct 11 2011 at 08:20:10 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 = 4165 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5450259 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): 2.342000 60.88800 ymin,ymax (A): -37.12800 24.37900 zmin,zma (A): -29.50900 35.80900 x,y,z range (A): 58.54600 61.50700 65.31800 scale (grids/A): 0.5450259 object centre (A): 31.61500 -6.374501 3.150002 number of atom coordinates read : 4165 total number of charged atoms : 4024 net assigned charge : 0.5000355 assigned positive charge : 624.1121 centred at (gu) : 87.99424 89.86467 90.18539 assigned negative charge : -623.6151 centred at (gu) : 88.01073 89.75082 90.15939 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8212 nv = 96 ne = 84 npr = 82003 no. pairs analyzed = 82003 no. exposed pairs = 5560 no. arc points = 39428 no. surface atoms = 1873 nbur = 2292 mkacc time = 0.1900000 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 = 1.540000 m= 346 mr = 4101 m= 0 mr = 15 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4055 ## 527 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 10752 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9600617E-10 2.7252423E-10 midg,1,midg; midg,igrid,midg -1.0409510E-09 9.9831876E-10 1,midg,midg; igrid,midg,midg 2.9172853E-10 -7.2297703E-11 gauss-seidel spectral radius is 0.9827489 estimated iterations to convergence 63 setup time was (sec) 0.6800000 now iterating at: 08:20:11 rms-change max change #iterations 8.4852882E-02 14.90663 at 10iterations 5.8188592E-03 0.7330501 at 20iterations 6.1911583E-04 0.1009026 at 30iterations 1.5820067E-04 3.0420303E-02 at 40iterations 5.1531340E-05 1.0164261E-02 at 50iterations finished qdiffx linear iterations at : 08:20:13 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 5.1531340E-05 1.0164261E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 08:20:14 3.495u 0.158s 0:04.01 90.7% 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 Tue Oct 11 2011 at 08:20:14 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 = 4165 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.635078 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): 2.342000 60.88800 ymin,ymax (A): -37.12800 24.37900 zmin,zma (A): -29.50900 35.80900 x,y,z range (A): 58.54600 61.50700 65.31800 scale (grids/A): 1.635078 object centre (A): 31.61500 -6.374501 3.150002 number of atom coordinates read : 4165 total number of charged atoms : 4024 net assigned charge : 0.5000355 assigned positive charge : 624.1121 centred at (gu) : 83.98114 89.59247 90.55482 assigned negative charge : -623.6151 centred at (gu) : 84.03159 89.25199 90.47778 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 90534 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39428 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 28093 mr = 60042 m= 3035 mr = 19053 m= 89 mr = 1421 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 41231 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 480 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 30842 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) : 0.5450259 object centre at (A) : 31.61500 -6.374501 3.150002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6235093E-02 -2.0810721E-02 midg,1,midg; midg,igrid,midg -1.4150809E-02 1.4326946E-02 1,midg,midg; igrid,midg,midg 2.1388581E-02 4.1941814E-03 gauss-seidel spectral radius is 0.9983277 estimated iterations to convergence 194 setup time was (sec) 0.9700000 now iterating at: 08:20:15 rms-change max change #iterations 4.037148 169.1630 at 10iterations 1.734118 59.15495 at 20iterations 0.7492778 22.94521 at 30iterations 0.3233549 11.08386 at 40iterations 0.1393809 4.464989 at 50iterations 6.0183425E-02 1.856529 at 60iterations 2.5926085E-02 0.8306675 at 70iterations 1.1280742E-02 0.3876724 at 80iterations 4.9066893E-03 0.1644778 at 90iterations 2.1600144E-03 6.5689087E-02 at 100iterations 9.7639824E-04 3.1694412E-02 at 110iterations 4.5912719E-04 1.7767906E-02 at 120iterations finished qdiffx linear iterations at : 08:20:21 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 4.5912719E-04 1.7767906E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 08:20:22 7.729u 0.149s 0:08.20 95.8% 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 Tue Oct 11 2011 at 08:20:22 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 = 4165 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.452616 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): 2.342000 60.88800 ymin,ymax (A): -37.12800 24.37900 zmin,zma (A): -29.50900 35.80900 x,y,z range (A): 58.54600 61.50700 65.31800 scale (grids/A): 2.452616 object centre (A): 31.61500 -6.374501 3.150002 number of atom coordinates read : 4165 total number of charged atoms : 4024 net assigned charge : 0.5000355 assigned positive charge : 624.1121 centred at (gu) : 80.97151 89.38839 90.83183 assigned negative charge : -623.6151 centred at (gu) : 81.04724 88.87782 90.71627 start vw surface at 0.1900000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 209733 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39428 grid for indexing accessible points = 1.400000 m= 97294 mr = 146985 m= 27867 mr = 76064 m= 4793 mr = 20661 m= 391 mr = 3077 m= 5 mr = 187 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 1.570000 number of dielectric boundary points 93109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 32142 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) : 1.635078 object centre at (A) : 31.61500 -6.374501 3.150002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2992057 -0.5634761 midg,1,midg; midg,igrid,midg -0.2017305 0.1615393 1,midg,midg; igrid,midg,midg 0.2789870 2.7629882E-02 gauss-seidel spectral radius is 0.9992238 estimated iterations to convergence 283 setup time was (sec) 1.880000 now iterating at: 08:20:24 rms-change max change #iterations 10.57307 345.8611 at 10iterations 6.204950 176.0401 at 20iterations 3.606973 87.52386 at 30iterations 2.083685 50.33711 at 40iterations 1.202909 29.10950 at 50iterations 0.6910582 13.36936 at 60iterations 0.3950676 7.475706 at 70iterations 0.2260505 4.472126 at 80iterations 0.1288711 2.415018 at 90iterations 7.3521674E-02 1.456974 at 100iterations 4.1800715E-02 0.7633619 at 110iterations 2.3771612E-02 0.4944000 at 120iterations 1.3555937E-02 0.2468352 at 130iterations 7.6982342E-03 0.1479645 at 140iterations 4.3797805E-03 8.0773354E-02 at 150iterations 2.4956011E-03 4.4347763E-02 at 160iterations 1.4235080E-03 2.5772095E-02 at 170iterations 8.1589492E-04 1.5170097E-02 at 180iterations finished qdiffx linear iterations at : 08:20:34 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 8.1589492E-04 1.5170097E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 08:20:35 12.513u 0.183s 0:13.06 97.1% 0+0k 0+0io 0pf+0w