Tue Oct 11 07:40:57 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 07:40:57 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2670 !!! WARNING: HIR 55 has a net charge of 0.5140 !!! WARNING: SEP 202 has a net charge of -0.4750 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: SEP 207 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: 0.6960874 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): -13.49600 37.64700 ymin,ymax (A): -22.60800 25.16700 zmin,zma (A): -5.856000 40.32000 x,y,z range (A): 51.14300 47.77500 46.17600 scale (grids/A): 0.6960874 object centre (A): 12.07550 1.279500 17.23200 number of atom coordinates read : 2670 total number of charged atoms : 2306 net assigned charge : 6.470008 assigned positive charge : 369.1302 centred at (gu) : 91.26757 88.76575 89.37543 assigned negative charge : -362.6607 centred at (gu) : 91.29491 88.77302 89.54836 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8076 nv = 96 ne = 84 npr = 49692 no. pairs analyzed = 49692 no. exposed pairs = 2940 no. arc points = 20244 no. surface atoms = 1006 nbur = 1664 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 488 mr = 4672 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1834 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9056 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3175219E-07 -3.2220008E-08 midg,1,midg; midg,igrid,midg 5.6210741E-08 3.0014728E-08 1,midg,midg; igrid,midg,midg 4.1684235E-08 3.6678497E-08 gauss-seidel spectral radius is 0.9892802 estimated iterations to convergence 79 setup time was (sec) 0.4000000 now iterating at: 07:40:57 rms-change max change #iterations 0.2064897 34.96025 at 10iterations 2.5496611E-02 2.899218 at 20iterations 3.8437359E-03 0.5191040 at 30iterations 7.9543825E-04 0.1120758 at 40iterations 2.1719745E-04 3.3466339E-02 at 50iterations finished qdiffx linear iterations at : 07:41:00 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.1719745E-04 3.3466339E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 07:41:01 3.417u 0.160s 0:03.89 91.7% 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 07:41:01 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2670 !!! WARNING: HIR 55 has a net charge of 0.5140 !!! WARNING: SEP 202 has a net charge of -0.4750 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: SEP 207 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: 2.088262 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): -13.49600 37.64700 ymin,ymax (A): -22.60800 25.16700 zmin,zma (A): -5.856000 40.32000 x,y,z range (A): 51.14300 47.77500 46.17600 scale (grids/A): 2.088262 object centre (A): 12.07550 1.279500 17.23200 number of atom coordinates read : 2670 total number of charged atoms : 2306 net assigned charge : 6.470008 assigned positive charge : 369.1302 centred at (gu) : 93.80229 86.29709 88.12595 assigned negative charge : -362.6607 centred at (gu) : 93.88465 86.31909 88.64497 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 85155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20244 grid for indexing accessible points = 1.400000 m= 34333 mr = 60659 m= 6543 mr = 26444 m= 509 mr = 4404 m= 7 mr = 232 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 34809 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 18286 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) : 0.6960874 object centre at (A) : 12.07550 1.279500 17.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2337158E-02 -1.7000746E-02 midg,1,midg; midg,igrid,midg 1.7431976E-02 2.3870803E-02 1,midg,midg; igrid,midg,midg 1.8064288E-02 4.8134804E-02 gauss-seidel spectral radius is 0.9988311 estimated iterations to convergence 232 setup time was (sec) 0.6600000 now iterating at: 07:41:01 rms-change max change #iterations 4.910306 227.9690 at 10iterations 2.435244 72.10793 at 20iterations 1.205836 36.71804 at 30iterations 0.6011841 20.58461 at 40iterations 0.2993820 9.041044 at 50iterations 0.1486544 5.149340 at 60iterations 7.4122250E-02 2.016296 at 70iterations 3.7116390E-02 1.080585 at 80iterations 1.8584576E-02 0.5389557 at 90iterations 9.3638878E-03 0.2946053 at 100iterations 4.7523752E-03 0.1469269 at 110iterations 2.4669992E-03 7.6904297E-02 at 120iterations finished qdiffx linear iterations at : 07:41:09 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.4669992E-03 7.6904297E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 07:41:09 7.947u 0.186s 0:08.43 96.3% 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 Tue Oct 11 2011 at 07:41:09 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2670 !!! WARNING: HIR 55 has a net charge of 0.5140 !!! WARNING: SEP 202 has a net charge of -0.4750 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: SEP 207 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: 3.132393 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): -13.49600 37.64700 ymin,ymax (A): -22.60800 25.16700 zmin,zma (A): -5.856000 40.32000 x,y,z range (A): 51.14300 47.77500 46.17600 scale (grids/A): 3.132393 object centre (A): 12.07550 1.279500 17.23200 number of atom coordinates read : 2670 total number of charged atoms : 2306 net assigned charge : 6.470008 assigned positive charge : 369.1302 centred at (gu) : 95.70343 84.44556 87.18890 assigned negative charge : -362.6607 centred at (gu) : 95.82690 84.47858 87.96750 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 196173 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20244 grid for indexing accessible points = 1.400000 m= 106834 mr = 145672 m= 44075 mr = 89787 m= 12259 mr = 36553 m= 2188 mr = 9529 m= 205 mr = 1546 m= 5 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 78532 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 18444 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) : 2.088262 object centre at (A) : 12.07550 1.279500 17.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5262062 -0.2065652 midg,1,midg; midg,igrid,midg 0.1213339 0.1889192 1,midg,midg; igrid,midg,midg 3.5403155E-02 0.2444001 gauss-seidel spectral radius is 0.9992996 estimated iterations to convergence 298 setup time was (sec) 1.530000 now iterating at: 07:41:11 rms-change max change #iterations 10.80651 451.4502 at 10iterations 6.356493 154.3636 at 20iterations 3.726096 72.53004 at 30iterations 2.187850 39.72945 at 40iterations 1.281890 28.16800 at 50iterations 0.7501574 13.63004 at 60iterations 0.4379678 7.804230 at 70iterations 0.2565511 4.390751 at 80iterations 0.1500386 2.532690 at 90iterations 8.7719910E-02 1.516611 at 100iterations 5.1440205E-02 0.8253212 at 110iterations 3.0231364E-02 0.5750732 at 120iterations 1.7863182E-02 0.2925596 at 130iterations 1.0668523E-02 0.1714478 at 140iterations 6.4943042E-03 0.1166115 at 150iterations 4.0644426E-03 6.7283630E-02 at 160iterations 2.6577499E-03 4.7950745E-02 at 170iterations 1.8318597E-03 3.2852173E-02 at 180iterations finished qdiffx linear iterations at : 07:41:22 total time elapsed so far: 13.00000 # loops : 180 mean,max change (kT/e) : 1.8318597E-03 3.2852173E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 07:41:23 13.129u 0.229s 0:13.64 97.8% 0+0k 0+0io 0pf+0w