Tue Oct 11 03:59:39 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 Tue Oct 11 2011 at 03:59:39 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6431797 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): -10.73200 36.92600 ymin,ymax (A): -25.81400 22.55600 zmin,zma (A): -9.971001 45.37900 x,y,z range (A): 47.65800 48.37000 55.35000 scale (grids/A): 0.6431797 object centre (A): 13.09700 -1.629000 17.70400 number of atom coordinates read : 2737 total number of charged atoms : 2585 net assigned charge : 1.140009 assigned positive charge : 410.9878 centred at (gu) : 89.92864 90.25356 91.73621 assigned negative charge : -409.8484 centred at (gu) : 89.67150 90.09686 91.67480 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7439 nv = 96 ne = 84 npr = 56516 no. pairs analyzed = 56516 no. exposed pairs = 3224 no. arc points = 22854 no. surface atoms = 1093 nbur = 1644 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 4226 m= 4 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2265 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9045 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5092610E-09 1.4379236E-08 midg,1,midg; midg,igrid,midg -1.8596364E-08 2.3578570E-08 1,midg,midg; igrid,midg,midg -3.4251475E-08 3.4637505E-08 gauss-seidel spectral radius is 0.9874825 estimated iterations to convergence 73 setup time was (sec) 0.6400000 now iterating at: 03:59:40 rms-change max change #iterations 0.1543021 25.34899 at 10iterations 1.5698818E-02 2.084923 at 20iterations 1.6943942E-03 0.2179794 at 30iterations 2.2029159E-04 3.3018112E-02 at 40iterations 4.5452223E-05 5.9432983E-03 at 50iterations finished qdiffx linear iterations at : 03:59:43 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 4.5452223E-05 5.9432983E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 03:59:44 4.114u 0.272s 0:04.68 93.5% 0+0k 0+0io 6pf+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 03:59:44 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.929539 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): -10.73200 36.92600 ymin,ymax (A): -25.81400 22.55600 zmin,zma (A): -9.971001 45.37900 x,y,z range (A): 47.65800 48.37000 55.35000 scale (grids/A): 1.929539 object centre (A): 13.09700 -1.629000 17.70400 number of atom coordinates read : 2737 total number of charged atoms : 2585 net assigned charge : 1.140009 assigned positive charge : 410.9878 centred at (gu) : 89.78530 90.76014 95.20789 assigned negative charge : -409.8484 centred at (gu) : 89.01443 90.29043 95.02385 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 80624 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22854 grid for indexing accessible points = 1.400000 m= 29590 mr = 56956 m= 4671 mr = 22153 m= 273 mr = 2895 m= 4 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 864 time to turn everything in is 0.7300000 number of dielectric boundary points 33057 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 20339 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) : 0.6431797 object centre at (A) : 13.09700 -1.629000 17.70400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3681858E-02 -1.4987792E-03 midg,1,midg; midg,igrid,midg -1.2372300E-02 3.0014969E-02 1,midg,midg; igrid,midg,midg -1.7565029E-02 5.4840785E-02 gauss-seidel spectral radius is 0.9986801 estimated iterations to convergence 218 setup time was (sec) 1.030000 now iterating at: 03:59:45 rms-change max change #iterations 4.469404 224.8687 at 10iterations 2.118176 69.81757 at 20iterations 1.007825 33.47492 at 30iterations 0.4800522 14.05001 at 40iterations 0.2282056 6.944651 at 50iterations 0.1081386 3.184608 at 60iterations 5.1477838E-02 1.569103 at 70iterations 2.4401864E-02 0.7376728 at 80iterations 1.1621050E-02 0.3967667 at 90iterations 5.5380766E-03 0.1610546 at 100iterations 2.6317069E-03 8.0230713E-02 at 110iterations 1.2531987E-03 3.7029266E-02 at 120iterations finished qdiffx linear iterations at : 03:59:53 total time elapsed so far: 9.380000 # loops : 120 mean,max change (kT/e) : 1.2531987E-03 3.7029266E-02 energy calculations done at 9.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.560000 DelPhi exited at 03:59:54 9.566u 0.293s 0:10.19 96.6% 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 03:59:54 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.894309 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): -10.73200 36.92600 ymin,ymax (A): -25.81400 22.55600 zmin,zma (A): -9.971001 45.37900 x,y,z range (A): 47.65800 48.37000 55.35000 scale (grids/A): 2.894309 object centre (A): 13.09700 -1.629000 17.70400 number of atom coordinates read : 2737 total number of charged atoms : 2585 net assigned charge : 1.140009 assigned positive charge : 410.9878 centred at (gu) : 89.67789 91.14001 97.81161 assigned negative charge : -409.8484 centred at (gu) : 88.52153 90.43561 97.53561 start vw surface at 0.1600000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 186810 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22854 grid for indexing accessible points = 1.400000 m= 95842 mr = 138079 m= 34808 mr = 79088 m= 8467 mr = 28184 m= 1238 mr = 6369 m= 80 mr = 837 m= 0 mr = 26 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 2950 time to turn everything in is 1.830000 number of dielectric boundary points 74662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 20674 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) : 1.929539 object centre at (A) : 13.09700 -1.629000 17.70400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8513362 0.1987568 midg,1,midg; midg,igrid,midg -0.1512902 0.3642981 1,midg,midg; igrid,midg,midg -0.1057916 0.5081488 gauss-seidel spectral radius is 0.9992673 estimated iterations to convergence 292 setup time was (sec) 2.150000 now iterating at: 03:59:57 rms-change max change #iterations 10.42686 437.2478 at 10iterations 6.105444 147.9282 at 20iterations 3.566446 81.03883 at 30iterations 2.076738 44.31452 at 40iterations 1.205440 29.40420 at 50iterations 0.6993040 13.09232 at 60iterations 0.4060062 7.311207 at 70iterations 0.2355286 4.135887 at 80iterations 0.1361934 2.463387 at 90iterations 7.8795262E-02 1.466677 at 100iterations 4.5574628E-02 0.7882795 at 110iterations 2.6410438E-02 0.4827442 at 120iterations 1.5312328E-02 0.2607517 at 130iterations 8.9027025E-03 0.1602936 at 140iterations 5.2104709E-03 0.1012421 at 150iterations 3.0828088E-03 5.5945396E-02 at 160iterations 1.8499476E-03 3.5750628E-02 at 170iterations 1.1411649E-03 2.0995140E-02 at 180iterations finished qdiffx linear iterations at : 04:00:10 total time elapsed so far: 15.97000 # loops : 180 mean,max change (kT/e) : 1.1411649E-03 2.0995140E-02 energy calculations done at 15.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.15000 DelPhi exited at 04:00:11 16.147u 0.341s 0:16.91 97.4% 0+0k 0+0io 0pf+0w