Sun Oct 9 08:18:46 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 08:18:46 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5614 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 0.5182101 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): -31.50200 27.91500 ymin,ymax (A): -13.44400 54.88500 zmin,zma (A): -32.07900 36.61900 x,y,z range (A): 59.41700 68.32899 68.69801 scale (grids/A): 0.5182101 object centre (A): -1.793500 20.72050 2.270000 number of atom coordinates read : 5614 total number of charged atoms : 5444 net assigned charge : -4.985986 assigned positive charge : 842.7627 centred at (gu) : 87.97503 90.02994 89.78809 assigned negative charge : -847.7556 centred at (gu) : 87.95132 89.93218 89.85650 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 9518 nv = 96 ne = 84 npr = 114307 no. pairs analyzed = 114307 no. exposed pairs = 7039 no. arc points = 48700 no. surface atoms = 2361 nbur = 3253 mkacc time = 0.3000000 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 = 1.652000 m= 338 mr = 4964 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 4886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4712 ## 621 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 12732 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0060831E-10 -3.6726355E-10 midg,1,midg; midg,igrid,midg -5.1076449E-10 3.1315533E-10 1,midg,midg; igrid,midg,midg -3.3472519E-10 4.1663239E-13 gauss-seidel spectral radius is 0.9810117 estimated iterations to convergence 60 setup time was (sec) 0.8900000 now iterating at: 08:18:47 rms-change max change #iterations 7.9887815E-02 12.31844 at 10iterations 5.0653876E-03 0.6904564 at 20iterations 6.4340181E-04 0.1389389 at 30iterations 1.8934162E-04 4.2480469E-02 at 40iterations 6.2674073E-05 1.3481140E-02 at 50iterations finished qdiffx linear iterations at : 08:18:51 total time elapsed so far: 4.670000 # loops : 50 mean,max change (kT/e) : 6.2674073E-05 1.3481140E-02 energy calculations done at 4.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.830000 DelPhi exited at 08:18:52 4.839u 0.398s 0:05.54 94.2% 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 Sun Oct 9 2011 at 08:18:52 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5614 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 1.554630 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): -31.50200 27.91500 ymin,ymax (A): -13.44400 54.88500 zmin,zma (A): -32.07900 36.61900 x,y,z range (A): 59.41700 68.32899 68.69801 scale (grids/A): 1.554630 object centre (A): -1.793500 20.72050 2.270000 number of atom coordinates read : 5614 total number of charged atoms : 5444 net assigned charge : -4.985986 assigned positive charge : 842.7627 centred at (gu) : 83.92309 90.08796 89.36225 assigned negative charge : -847.7556 centred at (gu) : 83.85361 89.79613 89.56912 start vw surface at 0.1900000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 107340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48700 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 31213 mr = 73910 m= 2719 mr = 20717 m= 64 mr = 1225 m= 0 mr = 4 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1079 time to turn everything in is 0.8900000 number of dielectric boundary points 45480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 619 ## 5 charges are in solution ## iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 41066 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) : 0.5182101 object centre at (A) : -1.793500 20.72050 2.270000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2863794E-03 -8.7757120E-03 midg,1,midg; midg,igrid,midg -3.2073925E-03 8.6254962E-03 1,midg,midg; igrid,midg,midg -1.7528061E-03 -4.8840529E-04 gauss-seidel spectral radius is 0.9982475 estimated iterations to convergence 190 setup time was (sec) 1.210000 now iterating at: 08:18:53 rms-change max change #iterations 4.322602 153.6450 at 10iterations 1.833971 54.92860 at 20iterations 0.7779308 23.15006 at 30iterations 0.3292898 9.579899 at 40iterations 0.1395953 4.238599 at 50iterations 5.9182029E-02 1.785702 at 60iterations 2.5268706E-02 0.7792044 at 70iterations 1.0740486E-02 0.3061981 at 80iterations 4.6094917E-03 0.1297913 at 90iterations 2.0073031E-03 6.5432549E-02 at 100iterations 8.8771101E-04 2.9502869E-02 at 110iterations 4.2039788E-04 1.7265320E-02 at 120iterations finished qdiffx linear iterations at : 08:19:03 total time elapsed so far: 11.08000 # loops : 120 mean,max change (kT/e) : 4.2039788E-04 1.7265320E-02 energy calculations done at 11.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.25000 DelPhi exited at 08:19:04 11.251u 0.481s 0:12.00 97.7% 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 Sun Oct 9 2011 at 08:19:04 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5614 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 2.331945 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): -31.50200 27.91500 ymin,ymax (A): -13.44400 54.88500 zmin,zma (A): -32.07900 36.61900 x,y,z range (A): 59.41700 68.32899 68.69801 scale (grids/A): 2.331945 object centre (A): -1.793500 20.72050 2.270000 number of atom coordinates read : 5614 total number of charged atoms : 5444 net assigned charge : -4.985986 assigned positive charge : 842.7627 centred at (gu) : 80.88412 90.13131 89.04287 assigned negative charge : -847.7556 centred at (gu) : 80.78033 89.69424 89.35373 start vw surface at 0.1900000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 250295 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48700 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 111790 mr = 181783 m= 28450 mr = 87172 m= 3884 mr = 20411 m= 225 mr = 2409 m= 2 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 1.380000 no. cavity mid-points inaccessible to solvent = 3997 time to turn everything in is 2.200000 number of dielectric boundary points 102787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 2.360000 number of grid points assigned charge 43436 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) : 1.554630 object centre at (A) : -1.793500 20.72050 2.270000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2740591 0.1027892 midg,1,midg; midg,igrid,midg -6.0283896E-02 0.1314780 1,midg,midg; igrid,midg,midg 5.1164474E-02 -8.5408678E-03 gauss-seidel spectral radius is 0.9992288 estimated iterations to convergence 284 setup time was (sec) 2.580000 now iterating at: 08:19:07 rms-change max change #iterations 11.67869 266.1198 at 10iterations 6.901199 147.0250 at 20iterations 4.048537 81.27444 at 30iterations 2.355343 45.81602 at 40iterations 1.367056 27.23701 at 50iterations 0.7902452 15.05087 at 60iterations 0.4563071 7.548378 at 70iterations 0.2622982 4.600170 at 80iterations 0.1505921 2.618098 at 90iterations 8.6498737E-02 1.496279 at 100iterations 4.9574628E-02 0.8279190 at 110iterations 2.8365623E-02 0.5038681 at 120iterations 1.6253369E-02 0.2828627 at 130iterations 9.3085971E-03 0.1637683 at 140iterations 5.3272326E-03 8.9542389E-02 at 150iterations 3.0620652E-03 5.0647318E-02 at 160iterations 1.7649047E-03 2.9376030E-02 at 170iterations 1.0279316E-03 1.6754150E-02 at 180iterations finished qdiffx linear iterations at : 08:19:24 total time elapsed so far: 20.15000 # loops : 180 mean,max change (kT/e) : 1.0279316E-03 1.6754150E-02 energy calculations done at 20.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.31000 DelPhi exited at 08:19:25 20.319u 0.473s 0:21.08 98.5% 0+0k 0+0io 0pf+0w