Tue Oct 11 06:39:04 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 06:39:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6726245 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): -20.56000 23.65500 ymin,ymax (A): -26.74300 10.72500 zmin,zma (A): -16.37400 36.55300 x,y,z range (A): 44.21500 37.46800 52.92700 scale (grids/A): 0.6726245 object centre (A): 1.547501 -8.009001 10.08950 number of atom coordinates read : 2056 total number of charged atoms : 1928 net assigned charge : 7.500009 assigned positive charge : 311.7690 centred at (gu) : 90.14664 90.85136 90.14890 assigned negative charge : -304.2692 centred at (gu) : 89.98054 90.83170 90.13671 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6188 nv = 96 ne = 84 npr = 41685 no. pairs analyzed = 41685 no. exposed pairs = 2441 no. arc points = 16896 no. surface atoms = 836 nbur = 1220 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 368 mr = 3514 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1721 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7239 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3293573E-08 3.0046582E-08 midg,1,midg; midg,igrid,midg 1.8979117E-08 3.6458825E-08 1,midg,midg; igrid,midg,midg -9.0962340E-09 6.3221826E-08 gauss-seidel spectral radius is 0.9884859 estimated iterations to convergence 76 setup time was (sec) 0.3600000 now iterating at: 06:39:05 rms-change max change #iterations 0.1581741 23.98920 at 10iterations 1.8152691E-02 2.753514 at 20iterations 2.0864324E-03 0.3037415 at 30iterations 2.8228428E-04 4.1160583E-02 at 40iterations 5.4527904E-05 8.5411072E-03 at 50iterations finished qdiffx linear iterations at : 06:39:07 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 5.4527904E-05 8.5411072E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 06:39:08 3.345u 0.158s 0:03.98 87.6% 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 06:39:08 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 = 2056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.017874 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): -20.56000 23.65500 ymin,ymax (A): -26.74300 10.72500 zmin,zma (A): -16.37400 36.55300 x,y,z range (A): 44.21500 37.46800 52.92700 scale (grids/A): 2.017874 object centre (A): 1.547501 -8.009001 10.08950 number of atom coordinates read : 2056 total number of charged atoms : 1928 net assigned charge : 7.500009 assigned positive charge : 311.7690 centred at (gu) : 90.43992 92.55408 90.44652 assigned negative charge : -304.2692 centred at (gu) : 89.94167 92.49526 90.41009 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 66670 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16896 grid for indexing accessible points = 1.400000 m= 25344 mr = 47239 m= 4311 mr = 19018 m= 293 mr = 2714 m= 5 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 27528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 15211 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) : 0.6726245 object centre at (A) : 1.547501 -8.009001 10.08950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8602743E-02 3.9178193E-02 midg,1,midg; midg,igrid,midg 5.7524121E-03 2.5844872E-02 1,midg,midg; igrid,midg,midg 5.3859781E-04 3.4594130E-02 gauss-seidel spectral radius is 0.9987157 estimated iterations to convergence 221 setup time was (sec) 0.5400000 now iterating at: 06:39:09 rms-change max change #iterations 4.119156 186.6853 at 10iterations 1.976074 72.07858 at 20iterations 0.9490556 32.46463 at 30iterations 0.4546467 15.91657 at 40iterations 0.2190004 7.100209 at 50iterations 0.1049809 3.231814 at 60iterations 5.0595406E-02 1.537255 at 70iterations 2.4223795E-02 0.7834616 at 80iterations 1.1706506E-02 0.3870964 at 90iterations 5.6465194E-03 0.1784048 at 100iterations 2.7365128E-03 8.9206696E-02 at 110iterations 1.3364423E-03 4.3998718E-02 at 120iterations finished qdiffx linear iterations at : 06:39:16 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 1.3364423E-03 4.3998718E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 06:39:17 7.660u 0.209s 0:08.40 93.5% 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 06:39:17 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 = 2056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.026810 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): -20.56000 23.65500 ymin,ymax (A): -26.74300 10.72500 zmin,zma (A): -16.37400 36.55300 x,y,z range (A): 44.21500 37.46800 52.92700 scale (grids/A): 3.026810 object centre (A): 1.547501 -8.009001 10.08950 number of atom coordinates read : 2056 total number of charged atoms : 1928 net assigned charge : 7.500009 assigned positive charge : 311.7690 centred at (gu) : 90.65994 93.83113 90.66970 assigned negative charge : -304.2692 centred at (gu) : 89.91260 93.74294 90.61523 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 153966 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16896 grid for indexing accessible points = 1.400000 m= 80751 mr = 114206 m= 30477 mr = 66832 m= 8052 mr = 24528 m= 1319 mr = 6044 m= 80 mr = 930 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 62068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 15424 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) : 2.017874 object centre at (A) : 1.547501 -8.009001 10.08950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9201503 0.3613619 midg,1,midg; midg,igrid,midg 4.3499492E-02 0.2189309 1,midg,midg; igrid,midg,midg 4.8296727E-02 0.2834396 gauss-seidel spectral radius is 0.9992636 estimated iterations to convergence 291 setup time was (sec) 1.090000 now iterating at: 06:39:18 rms-change max change #iterations 9.521632 336.0167 at 10iterations 5.570957 122.0551 at 20iterations 3.257832 93.99368 at 30iterations 1.899338 38.80317 at 40iterations 1.105439 29.58290 at 50iterations 0.6401763 13.36857 at 60iterations 0.3721719 7.554636 at 70iterations 0.2158189 4.538893 at 80iterations 0.1246428 2.412701 at 90iterations 7.2250292E-02 1.379120 at 100iterations 4.1891009E-02 0.8766308 at 110iterations 2.4307549E-02 0.4317570 at 120iterations 1.4144490E-02 0.2937717 at 130iterations 8.3221849E-03 0.1587930 at 140iterations 4.9390006E-03 0.1114807 at 150iterations 3.0099934E-03 6.5544128E-02 at 160iterations 1.9068564E-03 3.6060333E-02 at 170iterations 1.2621924E-03 2.4509430E-02 at 180iterations finished qdiffx linear iterations at : 06:39:29 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 1.2621924E-03 2.4509430E-02 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 06:39:29 12.280u 0.222s 0:12.77 97.8% 0+0k 0+0io 0pf+0w