Tue Oct 11 06:42:51 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 Tue Oct 11 2011 at 06:42:51 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1594 !!! WARNING: SEP 111 has a net charge of -0.4750 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: 0.7356740 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): 36.93200 81.27200 ymin,ymax (A): 6.737999 42.05500 zmin,zma (A): -12.03400 36.35700 x,y,z range (A): 44.33999 35.31700 48.39100 scale (grids/A): 0.7356740 object centre (A): 59.10200 24.39650 12.16150 number of atom coordinates read : 1594 total number of charged atoms : 1539 net assigned charge : 6.525005 assigned positive charge : 246.9556 centred at (gu) : 88.84062 89.48367 90.04391 assigned negative charge : -240.4304 centred at (gu) : 88.82603 89.39597 90.05692 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6088 nv = 96 ne = 84 npr = 29965 no. pairs analyzed = 29965 no. exposed pairs = 2161 no. arc points = 15140 no. surface atoms = 728 nbur = 866 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 395 mr = 3227 m= 2 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1390 ## 115 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6543 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1322069E-07 9.6735107E-08 midg,1,midg; midg,igrid,midg 4.7220826E-08 1.5062685E-07 1,midg,midg; igrid,midg,midg 1.1703471E-07 9.3422024E-08 gauss-seidel spectral radius is 0.9903216 estimated iterations to convergence 83 setup time was (sec) 0.4800000 now iterating at: 06:42:52 rms-change max change #iterations 0.2015412 27.37225 at 10iterations 2.6768669E-02 4.369555 at 20iterations 3.4880906E-03 0.5357776 at 30iterations 4.6394495E-04 7.2540283E-02 at 40iterations 6.1547667E-05 8.5449219E-03 at 50iterations finished qdiffx linear iterations at : 06:42:55 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 6.1547667E-05 8.5449219E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 06:42:55 3.440u 0.190s 0:03.95 91.8% 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 06:42:55 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1594 !!! WARNING: SEP 111 has a net charge of -0.4750 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: 2.207022 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): 36.93200 81.27200 ymin,ymax (A): 6.737999 42.05500 zmin,zma (A): -12.03400 36.35700 x,y,z range (A): 44.33999 35.31700 48.39100 scale (grids/A): 2.207022 object centre (A): 59.10200 24.39650 12.16150 number of atom coordinates read : 1594 total number of charged atoms : 1539 net assigned charge : 6.525005 assigned positive charge : 246.9556 centred at (gu) : 86.52214 88.45141 90.13219 assigned negative charge : -240.4304 centred at (gu) : 86.47830 88.18818 90.17114 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 63897 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15140 grid for indexing accessible points = 1.400000 m= 25583 mr = 43446 m= 5179 mr = 18961 m= 512 mr = 3256 m= 12 mr = 213 m= 0 mr = 6 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 29301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 12248 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) : 0.7356740 object centre at (A) : 59.10200 24.39650 12.16150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1746896E-02 4.1493811E-02 midg,1,midg; midg,igrid,midg -4.2189332E-03 2.8149953E-02 1,midg,midg; igrid,midg,midg 4.4823073E-02 3.0936863E-02 gauss-seidel spectral radius is 0.9988709 estimated iterations to convergence 236 setup time was (sec) 0.8400000 now iterating at: 06:42:56 rms-change max change #iterations 4.256515 186.8841 at 10iterations 2.124569 80.78391 at 20iterations 1.067789 36.43312 at 30iterations 0.5361621 21.25374 at 40iterations 0.2685594 9.402691 at 50iterations 0.1343201 4.436716 at 60iterations 6.7066759E-02 2.049464 at 70iterations 3.3701699E-02 1.040649 at 80iterations 1.6886165E-02 0.6365013 at 90iterations 8.4822169E-03 0.2735500 at 100iterations 4.2382879E-03 0.1390140 at 110iterations 2.1265659E-03 6.3143253E-02 at 120iterations finished qdiffx linear iterations at : 06:43:03 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 2.1265659E-03 6.3143253E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 06:43:04 7.847u 0.205s 0:08.42 95.4% 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 06:43:04 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1594 !!! WARNING: SEP 111 has a net charge of -0.4750 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: 3.310533 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): 36.93200 81.27200 ymin,ymax (A): 6.737999 42.05500 zmin,zma (A): -12.03400 36.35700 x,y,z range (A): 44.33999 35.31700 48.39100 scale (grids/A): 3.310533 object centre (A): 59.10200 24.39650 12.16150 number of atom coordinates read : 1594 total number of charged atoms : 1539 net assigned charge : 6.525005 assigned positive charge : 246.9556 centred at (gu) : 84.78336 87.67709 90.19849 assigned negative charge : -240.4304 centred at (gu) : 84.71768 87.28241 90.25684 start vw surface at 0.1400000 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 146841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15140 grid for indexing accessible points = 1.400000 m= 78701 mr = 104904 m= 32998 mr = 64404 m= 9800 mr = 26481 m= 1911 mr = 7223 m= 224 mr = 1295 m= 12 mr = 134 m= 0 mr = 4 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.640000 number of dielectric boundary points 66042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 12312 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) : 2.207022 object centre at (A) : 59.10200 24.39650 12.16150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2576929 0.3707112 midg,1,midg; midg,igrid,midg -6.5267704E-02 0.2183075 1,midg,midg; igrid,midg,midg 0.5714337 0.2706523 gauss-seidel spectral radius is 0.9993071 estimated iterations to convergence 300 setup time was (sec) 1.960000 now iterating at: 06:43:06 rms-change max change #iterations 9.410393 271.8329 at 10iterations 5.615308 119.3800 at 20iterations 3.331442 65.61407 at 30iterations 1.969774 39.22185 at 40iterations 1.163178 25.98594 at 50iterations 0.6869869 13.47039 at 60iterations 0.4025243 7.284626 at 70iterations 0.2367930 4.754529 at 80iterations 0.1394994 2.876899 at 90iterations 8.1926465E-02 1.690381 at 100iterations 4.7979962E-02 0.8612442 at 110iterations 2.8181149E-02 0.5673771 at 120iterations 1.6563533E-02 0.3130798 at 130iterations 9.7156893E-03 0.1827807 at 140iterations 5.7102400E-03 0.1050034 at 150iterations 3.3801591E-03 6.3903809E-02 at 160iterations 2.0028532E-03 4.1263580E-02 at 170iterations 1.2048756E-03 2.3227692E-02 at 180iterations finished qdiffx linear iterations at : 06:43:17 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 1.2048756E-03 2.3227692E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 06:43:18 12.949u 0.225s 0:13.84 95.0% 0+0k 0+0io 0pf+0w