Tue Oct 11 04:32:19 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 04:32:20 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2769 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6374217 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): -11.30900 36.30000 ymin,ymax (A): -25.82900 22.50000 zmin,zma (A): -10.44400 45.40600 x,y,z range (A): 47.60900 48.32900 55.85000 scale (grids/A): 0.6374217 object centre (A): 12.49550 -1.664500 17.48100 number of atom coordinates read : 2769 total number of charged atoms : 2616 net assigned charge : 2.154016 assigned positive charge : 420.7997 centred at (gu) : 90.15192 90.42520 92.05885 assigned negative charge : -418.6463 centred at (gu) : 89.91209 90.29027 91.98772 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7322 nv = 96 ne = 84 npr = 57051 no. pairs analyzed = 57051 no. exposed pairs = 3336 no. arc points = 23210 no. surface atoms = 1124 nbur = 1645 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 387 mr = 4110 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3561 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2296 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8977 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6277830E-09 1.7059680E-08 midg,1,midg; midg,igrid,midg -1.2157097E-08 1.9920625E-08 1,midg,midg; igrid,midg,midg -2.5258593E-08 3.0923754E-08 gauss-seidel spectral radius is 0.9872580 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 04:32:20 rms-change max change #iterations 0.1495169 19.41769 at 10iterations 1.4968541E-02 1.865417 at 20iterations 1.5288087E-03 0.2041225 at 30iterations 1.7329030E-04 2.9195786E-02 at 40iterations 2.7051645E-05 3.9824247E-03 at 50iterations finished qdiffx linear iterations at : 04:32:23 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.7051645E-05 3.9824247E-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) 3.370000 DelPhi exited at 04:32:23 3.376u 0.166s 0:03.86 91.4% 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 04:32:23 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2769 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.912265 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): -11.30900 36.30000 ymin,ymax (A): -25.82900 22.50000 zmin,zma (A): -10.44400 45.40600 x,y,z range (A): 47.60900 48.32900 55.85000 scale (grids/A): 1.912265 object centre (A): 12.49550 -1.664500 17.48100 number of atom coordinates read : 2769 total number of charged atoms : 2616 net assigned charge : 2.154016 assigned positive charge : 420.7997 centred at (gu) : 90.45530 91.27465 96.17599 assigned negative charge : -418.6463 centred at (gu) : 89.73595 90.87051 95.96295 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79591 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23210 grid for indexing accessible points = 1.400000 m= 28919 mr = 55957 m= 4496 mr = 21515 m= 280 mr = 2863 m= 5 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1688 time to turn everything in is 0.3900000 number of dielectric boundary points 32848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20568 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) : 0.6374217 object centre at (A) : 12.49550 -1.664500 17.48100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3257782E-02 1.6663371E-02 midg,1,midg; midg,igrid,midg -1.2321983E-02 1.3390334E-02 1,midg,midg; igrid,midg,midg -1.3880459E-02 5.4093018E-02 gauss-seidel spectral radius is 0.9986587 estimated iterations to convergence 216 setup time was (sec) 0.6000000 now iterating at: 04:32:24 rms-change max change #iterations 4.478334 205.9701 at 10iterations 2.111826 76.23943 at 20iterations 0.9997579 32.30717 at 30iterations 0.4713835 15.70304 at 40iterations 0.2225849 8.076069 at 50iterations 0.1048025 3.234009 at 60iterations 4.9662616E-02 1.444595 at 70iterations 2.3439432E-02 0.8271875 at 80iterations 1.1076776E-02 0.3091908 at 90iterations 5.2305241E-03 0.1567116 at 100iterations 2.4707755E-03 7.3064804E-02 at 110iterations 1.1753535E-03 3.5464764E-02 at 120iterations finished qdiffx linear iterations at : 04:32:31 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 1.1753535E-03 3.5464764E-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) 7.770000 DelPhi exited at 04:32:32 7.777u 0.206s 0:08.57 92.9% 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 04:32:32 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2769 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.868397 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): -11.30900 36.30000 ymin,ymax (A): -25.82900 22.50000 zmin,zma (A): -10.44400 45.40600 x,y,z range (A): 47.60900 48.32900 55.85000 scale (grids/A): 2.868397 object centre (A): 12.49550 -1.664500 17.48100 number of atom coordinates read : 2769 total number of charged atoms : 2616 net assigned charge : 2.154016 assigned positive charge : 420.7997 centred at (gu) : 90.68291 91.91177 99.26400 assigned negative charge : -418.6463 centred at (gu) : 89.60380 91.30566 98.94448 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 183788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23210 grid for indexing accessible points = 1.400000 m= 93975 mr = 135202 m= 34003 mr = 77345 m= 8096 mr = 27563 m= 1144 mr = 6081 m= 98 mr = 791 m= 0 mr = 46 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 5470 time to turn everything in is 1.020000 number of dielectric boundary points 74076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 20925 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) : 1.912265 object centre at (A) : 12.49550 -1.664500 17.48100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7003112 0.3945824 midg,1,midg; midg,igrid,midg -0.1440227 0.1500984 1,midg,midg; igrid,midg,midg -9.3867123E-02 0.4786704 gauss-seidel spectral radius is 0.9992623 estimated iterations to convergence 291 setup time was (sec) 1.250000 now iterating at: 04:32:34 rms-change max change #iterations 10.45256 365.5557 at 10iterations 6.110366 150.4894 at 20iterations 3.557229 76.13969 at 30iterations 2.075237 45.27791 at 40iterations 1.202103 23.98281 at 50iterations 0.6952565 13.46122 at 60iterations 0.4041567 7.807951 at 70iterations 0.2327762 4.469859 at 80iterations 0.1344620 2.447102 at 90iterations 7.7761993E-02 1.659704 at 100iterations 4.4938020E-02 0.8982925 at 110iterations 2.5967909E-02 0.5198517 at 120iterations 1.4980410E-02 0.2875137 at 130iterations 8.6759329E-03 0.1649740 at 140iterations 5.0184089E-03 8.4178448E-02 at 150iterations 2.9215238E-03 4.9760818E-02 at 160iterations 1.7143112E-03 3.1364441E-02 at 170iterations 1.0167944E-03 2.1221161E-02 at 180iterations finished qdiffx linear iterations at : 04:32:45 total time elapsed so far: 12.54000 # loops : 180 mean,max change (kT/e) : 1.0167944E-03 2.1221161E-02 energy calculations done at 12.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.67000 DelPhi exited at 04:32:46 12.674u 0.211s 0:13.54 95.1% 0+0k 0+0io 0pf+0w