Mon Oct 10 17:19:35 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 Mon Oct 10 2011 at 17:19:35 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4824 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5131975 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): -18.62200 36.51800 ymin,ymax (A): -30.83900 35.53300 zmin,zma (A): -3.967000 65.40200 x,y,z range (A): 55.14000 66.37200 69.36900 scale (grids/A): 0.5131975 object centre (A): 8.948001 2.347000 30.71750 number of atom coordinates read : 4824 total number of charged atoms : 4573 net assigned charge : 5.706028 assigned positive charge : 724.0701 centred at (gu) : 90.35640 90.25501 88.39835 assigned negative charge : -718.3688 centred at (gu) : 90.23296 90.27064 88.39813 start vw surface at 0.2300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 8114 nv = 96 ne = 84 npr = 97747 no. pairs analyzed = 97747 no. exposed pairs = 6145 no. arc points = 41922 no. surface atoms = 2063 nbur = 2761 mkacc time = 0.3300000 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= 268 mr = 4181 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 4196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4023 ## 557 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 10629 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3412293E-10 6.0152335E-11 midg,1,midg; midg,igrid,midg 1.2621790E-10 4.6804616E-11 1,midg,midg; igrid,midg,midg -2.4991595E-10 4.8607657E-10 gauss-seidel spectral radius is 0.9805857 estimated iterations to convergence 59 setup time was (sec) 1.000000 now iterating at: 17:19:36 rms-change max change #iterations 7.0638411E-02 10.04433 at 10iterations 5.2340659E-03 1.034798 at 20iterations 1.0342853E-03 0.1517563 at 30iterations 3.7161421E-04 4.6952248E-02 at 40iterations 1.5011788E-04 2.0162225E-02 at 50iterations finished qdiffx linear iterations at : 17:19:40 total time elapsed so far: 4.910000 # loops : 50 mean,max change (kT/e) : 1.5011788E-04 2.0162225E-02 energy calculations done at 4.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.130000 DelPhi exited at 17:19:41 5.133u 0.424s 0:05.92 93.7% 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 Mon Oct 10 2011 at 17:19:41 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4824 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.539593 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): -18.62200 36.51800 ymin,ymax (A): -30.83900 35.53300 zmin,zma (A): -3.967000 65.40200 x,y,z range (A): 55.14000 66.37200 69.36900 scale (grids/A): 1.539593 object centre (A): 8.948001 2.347000 30.71750 number of atom coordinates read : 4824 total number of charged atoms : 4573 net assigned charge : 5.706028 assigned positive charge : 724.0701 centred at (gu) : 91.06765 90.76356 85.19379 assigned negative charge : -718.3688 centred at (gu) : 90.69864 90.81174 85.19407 start vw surface at 0.2200000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 91058 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41922 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26506 mr = 62649 m= 2378 mr = 17452 m= 62 mr = 991 m= 0 mr = 5 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9500000 number of dielectric boundary points 38907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 527 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 34412 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) : 0.5131975 object centre at (A) : 8.948001 2.347000 30.71750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1709077E-03 1.7327979E-02 midg,1,midg; midg,igrid,midg -2.7100367E-03 -1.0375777E-02 1,midg,midg; igrid,midg,midg -1.4351676E-03 1.3462244E-02 gauss-seidel spectral radius is 0.9981410 estimated iterations to convergence 184 setup time was (sec) 1.290000 now iterating at: 17:19:43 rms-change max change #iterations 3.851874 150.5142 at 10iterations 1.593920 48.95211 at 20iterations 0.6566409 21.07071 at 30iterations 0.2718182 10.28615 at 40iterations 0.1124693 3.581635 at 50iterations 4.6691019E-02 1.615747 at 60iterations 1.9337883E-02 0.6917267 at 70iterations 8.0874730E-03 0.2525826 at 80iterations 3.4362974E-03 0.1081533 at 90iterations 1.5129519E-03 4.5387268E-02 at 100iterations 7.2445342E-04 2.2781372E-02 at 110iterations 3.9822189E-04 1.5377522E-02 at 120iterations finished qdiffx linear iterations at : 17:19:53 total time elapsed so far: 11.23000 # loops : 120 mean,max change (kT/e) : 3.9822189E-04 1.5377522E-02 energy calculations done at 11.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.45000 DelPhi exited at 17:19:54 11.450u 0.498s 0:12.51 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 Mon Oct 10 2011 at 17:19:54 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4824 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.309389 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): -18.62200 36.51800 ymin,ymax (A): -30.83900 35.53300 zmin,zma (A): -3.967000 65.40200 x,y,z range (A): 55.14000 66.37200 69.36900 scale (grids/A): 2.309389 object centre (A): 8.948001 2.347000 30.71750 number of atom coordinates read : 4824 total number of charged atoms : 4573 net assigned charge : 5.706028 assigned positive charge : 724.0701 centred at (gu) : 91.60113 91.14506 82.79014 assigned negative charge : -718.3688 centred at (gu) : 91.04782 91.21764 82.79109 start vw surface at 0.2300000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 212665 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41922 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 94974 mr = 154241 m= 23606 mr = 73997 m= 3400 mr = 16708 m= 202 mr = 2019 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 1.440000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.340000 number of dielectric boundary points 87819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 2.520000 number of grid points assigned charge 36488 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) : 1.539593 object centre at (A) : 8.948001 2.347000 30.71750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1186722 0.4610130 midg,1,midg; midg,igrid,midg -0.2034532 -0.2716966 1,midg,midg; igrid,midg,midg -1.3655382E-02 0.2002339 gauss-seidel spectral radius is 0.9991723 estimated iterations to convergence 274 setup time was (sec) 2.750000 now iterating at: 17:19:57 rms-change max change #iterations 10.44920 322.0123 at 10iterations 6.036749 136.9856 at 20iterations 3.451697 71.40431 at 30iterations 1.961331 48.25908 at 40iterations 1.111638 24.69149 at 50iterations 0.6266592 12.00968 at 60iterations 0.3534340 7.446843 at 70iterations 0.1984639 4.272707 at 80iterations 0.1114956 2.145785 at 90iterations 6.2164124E-02 1.152641 at 100iterations 3.4932375E-02 0.6585541 at 110iterations 1.9533638E-02 0.3534145 at 120iterations 1.0943031E-02 0.2049522 at 130iterations 6.1380626E-03 0.1128323 at 140iterations 3.4497569E-03 7.1502686E-02 at 150iterations 1.9587383E-03 4.1160583E-02 at 160iterations 1.1268205E-03 1.9855499E-02 at 170iterations 6.6578505E-04 1.3749838E-02 at 180iterations finished qdiffx linear iterations at : 17:20:14 total time elapsed so far: 20.20000 # loops : 180 mean,max change (kT/e) : 6.6578505E-04 1.3749838E-02 energy calculations done at 20.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.42000 DelPhi exited at 17:20:15 20.420u 0.503s 0:21.28 98.3% 0+0k 0+0io 0pf+0w