Sun Oct 9 22:09:59 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 22:09:59 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6330127 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): 45.37700 98.40100 ymin,ymax (A): 2.955000 59.19400 zmin,zma (A): 14.90500 67.37600 x,y,z range (A): 53.02400 56.23900 52.47100 scale (grids/A): 0.6330127 object centre (A): 71.88900 31.07450 41.14050 number of atom coordinates read : 3253 total number of charged atoms : 3103 net assigned charge : 7.200016 assigned positive charge : 495.4706 centred at (gu) : 90.39932 88.09312 90.48948 assigned negative charge : -488.2721 centred at (gu) : 90.33276 88.05048 90.48980 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8801 nv = 96 ne = 84 npr = 64087 no. pairs analyzed = 64087 no. exposed pairs = 4086 no. arc points = 29689 no. surface atoms = 1380 nbur = 1873 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 435 mr = 4663 m= 4 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2200000 number of dielectric boundary points 4528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2996 ## 309 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 10703 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8007929E-09 9.4834665E-09 midg,1,midg; midg,igrid,midg 4.9574878E-09 9.1775947E-09 1,midg,midg; igrid,midg,midg 5.0953530E-10 1.8047665E-08 gauss-seidel spectral radius is 0.9871379 estimated iterations to convergence 72 setup time was (sec) 0.4100000 now iterating at: 22:09:59 rms-change max change #iterations 0.1589554 24.51377 at 10iterations 1.5226217E-02 1.959366 at 20iterations 1.4700925E-03 0.1928406 at 30iterations 1.4450382E-04 1.9450188E-02 at 40iterations 1.4302793E-05 1.8920898E-03 at 50iterations finished qdiffx linear iterations at : 22:10:02 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.4302793E-05 1.8920898E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 22:10:03 3.432u 0.197s 0:04.02 90.0% 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 22:10:03 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.899038 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): 45.37700 98.40100 ymin,ymax (A): 2.955000 59.19400 zmin,zma (A): 14.90500 67.37600 x,y,z range (A): 53.02400 56.23900 52.47100 scale (grids/A): 1.899038 object centre (A): 71.88900 31.07450 41.14050 number of atom coordinates read : 3253 total number of charged atoms : 3103 net assigned charge : 7.200016 assigned positive charge : 495.4706 centred at (gu) : 91.19687 84.27856 91.46743 assigned negative charge : -488.2721 centred at (gu) : 90.99803 84.15116 91.46920 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 94840 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29689 grid for indexing accessible points = 1.400000 m= 32470 mr = 64610 m= 4965 mr = 23278 m= 382 mr = 2924 m= 14 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2111 time to turn everything in is 0.4500000 number of dielectric boundary points 41698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 24406 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) : 0.6330127 object centre at (A) : 71.88900 31.07450 41.14050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9648526E-03 -8.1696995E-03 midg,1,midg; midg,igrid,midg 8.6166367E-02 3.9038174E-02 1,midg,midg; igrid,midg,midg -2.1884255E-02 2.0497961E-02 gauss-seidel spectral radius is 0.9987002 estimated iterations to convergence 220 setup time was (sec) 0.6700000 now iterating at: 22:10:04 rms-change max change #iterations 4.796676 159.1306 at 10iterations 2.271407 73.85424 at 20iterations 1.083974 28.80435 at 30iterations 0.5165840 15.86302 at 40iterations 0.2458830 7.510339 at 50iterations 0.1172000 3.318874 at 60iterations 5.5873014E-02 1.692775 at 70iterations 2.6597830E-02 0.9799957 at 80iterations 1.2707404E-02 0.3653374 at 90iterations 6.0516372E-03 0.1731739 at 100iterations 2.8846154E-03 8.3393574E-02 at 110iterations 1.3764611E-03 4.0859222E-02 at 120iterations finished qdiffx linear iterations at : 22:10:11 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 1.3764611E-03 4.0859222E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 22:10:12 8.129u 0.227s 0:08.75 95.3% 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 22:10:12 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.848557 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): 45.37700 98.40100 ymin,ymax (A): 2.955000 59.19400 zmin,zma (A): 14.90500 67.37600 x,y,z range (A): 53.02400 56.23900 52.47100 scale (grids/A): 2.848557 object centre (A): 71.88900 31.07450 41.14050 number of atom coordinates read : 3253 total number of charged atoms : 3103 net assigned charge : 7.200016 assigned positive charge : 495.4706 centred at (gu) : 91.79504 81.41762 92.20093 assigned negative charge : -488.2721 centred at (gu) : 91.49719 81.22638 92.20362 start vw surface at 0.1000000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 219490 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29689 grid for indexing accessible points = 1.400000 m= 106234 mr = 156984 m= 36978 mr = 85725 m= 8849 mr = 28924 m= 1471 mr = 6391 m= 125 mr = 987 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 7254 time to turn everything in is 1.180000 number of dielectric boundary points 94079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 24823 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) : 1.899038 object centre at (A) : 71.88900 31.07450 41.14050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1775682E-02 -0.2348240 midg,1,midg; midg,igrid,midg 0.6610467 0.4223167 1,midg,midg; igrid,midg,midg -0.2882451 0.2519542 gauss-seidel spectral radius is 0.9992950 estimated iterations to convergence 297 setup time was (sec) 1.430000 now iterating at: 22:10:13 rms-change max change #iterations 11.33879 424.8815 at 10iterations 6.764571 156.4888 at 20iterations 4.012341 90.05376 at 30iterations 2.368392 56.81090 at 40iterations 1.392404 28.62566 at 50iterations 0.8174487 15.44034 at 60iterations 0.4793677 9.334219 at 70iterations 0.2807627 5.241781 at 80iterations 0.1642337 3.073109 at 90iterations 9.6057668E-02 1.667721 at 100iterations 5.6089703E-02 0.9829096 at 110iterations 3.2687180E-02 0.6428909 at 120iterations 1.9093962E-02 0.3226328 at 130iterations 1.1133097E-02 0.2016201 at 140iterations 6.5107774E-03 0.1009827 at 150iterations 3.7875460E-03 6.3426971E-02 at 160iterations 2.2119635E-03 3.9894104E-02 at 170iterations 1.2912488E-03 2.0761490E-02 at 180iterations finished qdiffx linear iterations at : 22:10:25 total time elapsed so far: 13.34000 # loops : 180 mean,max change (kT/e) : 1.2912488E-03 2.0761490E-02 energy calculations done at 13.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 22:10:26 13.483u 0.205s 0:14.00 97.7% 0+0k 0+0io 0pf+0w