Sat Oct 8 18:27:34 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 Sat Oct 8 2011 at 18:27:34 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2574 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: LYS 261 has a net charge of 1.5000 !!! WARNING: ZN5 556 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6226824 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): -32.06000 17.67200 ymin,ymax (A): -23.91100 23.02600 zmin,zma (A): -12.34400 44.82800 x,y,z range (A): 49.73200 46.93700 57.17200 scale (grids/A): 0.6226824 object centre (A): -7.193998 -0.4425001 16.24200 number of atom coordinates read : 2574 total number of charged atoms : 2473 net assigned charge : 6.000007 assigned positive charge : 394.6670 centred at (gu) : 88.50887 89.28578 89.87297 assigned negative charge : -388.6675 centred at (gu) : 88.43427 89.35381 89.71214 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6653 nv = 96 ne = 84 npr = 52043 no. pairs analyzed = 52043 no. exposed pairs = 3046 no. arc points = 22111 no. surface atoms = 1024 nbur = 1550 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 351 mr = 3743 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 123 time to turn everything in is 0.1900000 number of dielectric boundary points 3210 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2206 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8207 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6321313E-09 1.6180705E-08 midg,1,midg; midg,igrid,midg 1.1865478E-08 3.7115952E-10 1,midg,midg; igrid,midg,midg -2.5381233E-10 7.6924884E-09 gauss-seidel spectral radius is 0.9866404 estimated iterations to convergence 71 setup time was (sec) 0.4100000 now iterating at: 18:27:34 rms-change max change #iterations 0.1304100 20.19682 at 10iterations 1.2125984E-02 1.844955 at 20iterations 1.1247512E-03 0.1846366 at 30iterations 1.0432612E-04 1.3351440E-02 at 40iterations 9.9518275E-06 1.2969971E-03 at 50iterations finished qdiffx linear iterations at : 18:27:37 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 9.9518275E-06 1.2969971E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 18:27:38 3.525u 0.176s 0:04.05 91.1% 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 Sat Oct 8 2011 at 18:27:38 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2574 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: LYS 261 has a net charge of 1.5000 !!! WARNING: ZN5 556 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.868047 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): -32.06000 17.67200 ymin,ymax (A): -23.91100 23.02600 zmin,zma (A): -12.34400 44.82800 x,y,z range (A): 49.73200 46.93700 57.17200 scale (grids/A): 1.868047 object centre (A): -7.193998 -0.4425001 16.24200 number of atom coordinates read : 2574 total number of charged atoms : 2473 net assigned charge : 6.000007 assigned positive charge : 394.6670 centred at (gu) : 85.52613 87.85665 89.61825 assigned negative charge : -388.6675 centred at (gu) : 85.30265 88.06124 89.13627 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72268 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22111 grid for indexing accessible points = 1.400000 m= 26036 mr = 50390 m= 3919 mr = 19537 m= 238 mr = 2575 m= 1 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4576 time to turn everything in is 0.3500000 number of dielectric boundary points 29862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19363 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) : 0.6226824 object centre at (A) : -7.193998 -0.4425001 16.24200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4402069E-02 3.7736274E-02 midg,1,midg; midg,igrid,midg 1.7216142E-02 3.4431629E-03 1,midg,midg; igrid,midg,midg -5.1342306E-04 3.5061292E-02 gauss-seidel spectral radius is 0.9985810 estimated iterations to convergence 210 setup time was (sec) 0.5700000 now iterating at: 18:27:39 rms-change max change #iterations 4.081796 166.3959 at 10iterations 1.873612 63.59147 at 20iterations 0.8662261 32.58541 at 30iterations 0.3970501 13.28980 at 40iterations 0.1842456 6.023888 at 50iterations 8.5023716E-02 2.520805 at 60iterations 3.9358366E-02 1.242386 at 70iterations 1.8178215E-02 0.6520519 at 80iterations 8.3600730E-03 0.2626801 at 90iterations 3.8704884E-03 0.1210022 at 100iterations 1.7794239E-03 6.1527252E-02 at 110iterations 8.2516437E-04 2.7743340E-02 at 120iterations finished qdiffx linear iterations at : 18:27:46 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 8.2516437E-04 2.7743340E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 18:27:47 8.124u 0.231s 0:08.65 96.5% 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 Sat Oct 8 2011 at 18:27:47 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2574 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: LYS 261 has a net charge of 1.5000 !!! WARNING: ZN5 556 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.802071 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): -32.06000 17.67200 ymin,ymax (A): -23.91100 23.02600 zmin,zma (A): -12.34400 44.82800 x,y,z range (A): 49.73200 46.93700 57.17200 scale (grids/A): 2.802071 object centre (A): -7.193998 -0.4425001 16.24200 number of atom coordinates read : 2574 total number of charged atoms : 2473 net assigned charge : 6.000007 assigned positive charge : 394.6670 centred at (gu) : 83.28908 86.78470 89.42722 assigned negative charge : -388.6675 centred at (gu) : 82.95397 87.09174 88.70435 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 166963 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22111 grid for indexing accessible points = 1.400000 m= 84753 mr = 121637 m= 30009 mr = 70194 m= 7145 mr = 24496 m= 1109 mr = 5542 m= 66 mr = 847 m= 0 mr = 33 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 15668 time to turn everything in is 0.9300000 number of dielectric boundary points 67296 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 19775 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) : 1.868047 object centre at (A) : -7.193998 -0.4425001 16.24200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2062466 0.4288034 midg,1,midg; midg,igrid,midg 0.1995927 3.5022810E-02 1,midg,midg; igrid,midg,midg -1.6478398E-03 0.4326399 gauss-seidel spectral radius is 0.9992396 estimated iterations to convergence 286 setup time was (sec) 1.190000 now iterating at: 18:27:48 rms-change max change #iterations 9.505455 266.8715 at 10iterations 5.446639 112.8281 at 20iterations 3.117302 58.94683 at 30iterations 1.777474 31.83283 at 40iterations 1.013783 18.88158 at 50iterations 0.5767424 10.35945 at 60iterations 0.3287584 6.332380 at 70iterations 0.1868566 3.518612 at 80iterations 0.1063866 1.940628 at 90iterations 6.0454812E-02 1.139648 at 100iterations 3.4465417E-02 0.6453152 at 110iterations 1.9649601E-02 0.3507214 at 120iterations 1.1182483E-02 0.2070580 at 130iterations 6.3657947E-03 0.1183338 at 140iterations 3.6179319E-03 6.3663483E-02 at 150iterations 2.0609321E-03 4.2468071E-02 at 160iterations 1.1749389E-03 1.9851685E-02 at 170iterations 6.6752319E-04 1.2437820E-02 at 180iterations finished qdiffx linear iterations at : 18:28:00 total time elapsed so far: 13.29000 # loops : 180 mean,max change (kT/e) : 6.6752319E-04 1.2437820E-02 energy calculations done at 13.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.42000 DelPhi exited at 18:28:01 13.420u 0.262s 0:13.96 97.9% 0+0k 0+0io 0pf+0w