Tue Oct 11 04:17:11 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 04:17:11 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 = 2789 !!! WARNING: ASP 291 has a net charge of -0.2720 !!! 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: 0.6569842 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): -8.512000 40.66700 ymin,ymax (A): -26.45400 22.08800 zmin,zma (A): -9.625999 44.56100 x,y,z range (A): 49.17900 48.54200 54.18700 scale (grids/A): 0.6569842 object centre (A): 16.07750 -2.183001 17.46750 number of atom coordinates read : 2789 total number of charged atoms : 2637 net assigned charge : 2.868024 assigned positive charge : 420.9254 centred at (gu) : 89.97948 90.41140 88.47980 assigned negative charge : -418.0583 centred at (gu) : 90.20621 90.25636 88.54466 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7971 nv = 96 ne = 84 npr = 57421 no. pairs analyzed = 57421 no. exposed pairs = 3461 no. arc points = 23770 no. surface atoms = 1167 nbur = 1622 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 464 mr = 4487 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2900000 number of dielectric boundary points 3897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2301 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9525 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6321080E-08 -4.5794724E-09 midg,1,midg; midg,igrid,midg -2.2513209E-08 3.9747427E-08 1,midg,midg; igrid,midg,midg 5.0200494E-08 -3.9130953E-08 gauss-seidel spectral radius is 0.9880054 estimated iterations to convergence 75 setup time was (sec) 0.5100000 now iterating at: 04:17:12 rms-change max change #iterations 0.1685454 21.23855 at 10iterations 1.8327784E-02 2.499382 at 20iterations 1.9832673E-03 0.2615509 at 30iterations 2.4627667E-04 3.8547516E-02 at 40iterations 4.3498905E-05 6.7901611E-03 at 50iterations finished qdiffx linear iterations at : 04:17:14 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 4.3498905E-05 6.7901611E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 04:17:15 3.109u 0.155s 0:03.84 84.6% 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 04:17:15 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 = 2789 !!! WARNING: ASP 291 has a net charge of -0.2720 !!! 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: 1.970953 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): -8.512000 40.66700 ymin,ymax (A): -26.45400 22.08800 zmin,zma (A): -9.625999 44.56100 x,y,z range (A): 49.17900 48.54200 54.18700 scale (grids/A): 1.970953 object centre (A): 16.07750 -2.183001 17.46750 number of atom coordinates read : 2789 total number of charged atoms : 2637 net assigned charge : 2.868024 assigned positive charge : 420.9254 centred at (gu) : 89.93754 91.23353 85.43882 assigned negative charge : -418.0583 centred at (gu) : 90.61823 90.76881 85.63357 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 85842 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23770 grid for indexing accessible points = 1.400000 m= 31885 mr = 60474 m= 5356 mr = 23609 m= 348 mr = 3308 m= 2 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 479 time to turn everything in is 0.5800000 number of dielectric boundary points 35914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 20808 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) : 0.6569842 object centre at (A) : 16.07750 -2.183001 17.46750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1212862E-03 -6.2057458E-02 midg,1,midg; midg,igrid,midg -1.5505590E-02 3.2589927E-02 1,midg,midg; igrid,midg,midg 7.1625464E-02 -3.5328066E-03 gauss-seidel spectral radius is 0.9987391 estimated iterations to convergence 223 setup time was (sec) 0.8300000 now iterating at: 04:17:16 rms-change max change #iterations 4.752224 214.7154 at 10iterations 2.292640 75.73072 at 20iterations 1.107091 35.03855 at 30iterations 0.5359955 16.81057 at 40iterations 0.2586007 7.186838 at 50iterations 0.1252430 4.239511 at 60iterations 6.0352370E-02 1.854764 at 70iterations 2.9212307E-02 0.8397903 at 80iterations 1.4091655E-02 0.4061327 at 90iterations 6.8298695E-03 0.1913605 at 100iterations 3.2988386E-03 9.7081184E-02 at 110iterations 1.6013427E-03 4.6430111E-02 at 120iterations finished qdiffx linear iterations at : 04:17:22 total time elapsed so far: 6.750000 # loops : 120 mean,max change (kT/e) : 1.6013427E-03 4.6430111E-02 energy calculations done at 6.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 04:17:23 6.923u 0.205s 0:07.64 93.1% 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 Tue Oct 11 2011 at 04:17:23 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2789 !!! WARNING: ASP 291 has a net charge of -0.2720 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.956429 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): -8.512000 40.66700 ymin,ymax (A): -26.45400 22.08800 zmin,zma (A): -9.625999 44.56100 x,y,z range (A): 49.17900 48.54200 54.18700 scale (grids/A): 2.956429 object centre (A): 16.07750 -2.183001 17.46750 number of atom coordinates read : 2789 total number of charged atoms : 2637 net assigned charge : 2.868024 assigned positive charge : 420.9254 centred at (gu) : 89.90625 91.85025 83.15792 assigned negative charge : -418.0583 centred at (gu) : 90.92735 91.15323 83.45027 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 198460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23770 grid for indexing accessible points = 1.400000 m= 102582 mr = 146364 m= 38056 mr = 84225 m= 9491 mr = 30661 m= 1446 mr = 7012 m= 94 mr = 926 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 1746 time to turn everything in is 1.510000 number of dielectric boundary points 80902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 21088 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) : 1.970953 object centre at (A) : 16.07750 -2.183001 17.46750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2657200 -0.9508560 midg,1,midg; midg,igrid,midg -0.1770987 0.3800063 1,midg,midg; igrid,midg,midg 0.6215504 -1.6922049E-02 gauss-seidel spectral radius is 0.9992853 estimated iterations to convergence 295 setup time was (sec) 1.800000 now iterating at: 04:17:25 rms-change max change #iterations 10.86216 369.2825 at 10iterations 6.384919 137.5321 at 20iterations 3.751362 79.24300 at 30iterations 2.195455 44.52522 at 40iterations 1.285487 23.49476 at 50iterations 0.7519342 14.43575 at 60iterations 0.4385554 7.929192 at 70iterations 0.2558747 4.635587 at 80iterations 0.1489215 2.535851 at 90iterations 8.6691044E-02 1.516539 at 100iterations 5.0619494E-02 0.9057879 at 110iterations 2.9442558E-02 0.5189667 at 120iterations 1.7163554E-02 0.2881241 at 130iterations 9.9826353E-03 0.1933880 at 140iterations 5.8596698E-03 0.1071415 at 150iterations 3.4438749E-03 5.6846619E-02 at 160iterations 2.0404975E-03 3.8805008E-02 at 170iterations 1.2257989E-03 2.3300171E-02 at 180iterations finished qdiffx linear iterations at : 04:17:34 total time elapsed so far: 11.21000 # loops : 180 mean,max change (kT/e) : 1.2257989E-03 2.3300171E-02 energy calculations done at 11.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.38000 DelPhi exited at 04:17:35 11.380u 0.193s 0:12.21 94.7% 0+0k 0+0io 0pf+0w