Sat Oct 8 13:32:31 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 Sat Oct 8 2011 at 13:32:31 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2988 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 350 has a net charge of -2.0000 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: 0.6364986 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): -23.50200 27.36400 ymin,ymax (A): -25.14600 27.24200 zmin,zma (A): -23.02800 32.90300 x,y,z range (A): 50.86600 52.38800 55.93100 scale (grids/A): 0.6364986 object centre (A): 1.931000 1.047999 4.937500 number of atom coordinates read : 2988 total number of charged atoms : 2842 net assigned charge : 1.4009014E-02 assigned positive charge : 448.5726 centred at (gu) : 88.74236 89.01208 87.53643 assigned negative charge : -448.5594 centred at (gu) : 88.69717 88.99233 87.63470 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8019 nv = 96 ne = 84 npr = 61660 no. pairs analyzed = 61660 no. exposed pairs = 3841 no. arc points = 26201 no. surface atoms = 1292 nbur = 1696 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 469 mr = 4386 m= 3 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4035 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2564 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9866 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0066947E-08 -7.1945458E-09 midg,1,midg; midg,igrid,midg -3.2366128E-09 1.7669339E-09 1,midg,midg; igrid,midg,midg -7.5402946E-09 3.9970223E-09 gauss-seidel spectral radius is 0.9872452 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 13:32:32 rms-change max change #iterations 0.1586708 23.44533 at 10iterations 1.6137898E-02 2.158157 at 20iterations 1.9921069E-03 0.2494144 at 30iterations 5.1398150E-04 6.7842484E-02 at 40iterations 1.9380762E-04 2.4324417E-02 at 50iterations finished qdiffx linear iterations at : 13:32:34 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 1.9380762E-04 2.4324417E-02 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 13:32:35 3.114u 0.140s 0:03.53 92.0% 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 13:32:35 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2988 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 350 has a net charge of -2.0000 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: 1.909496 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): -23.50200 27.36400 ymin,ymax (A): -25.14600 27.24200 zmin,zma (A): -23.02800 32.90300 x,y,z range (A): 50.86600 52.38800 55.93100 scale (grids/A): 1.909496 object centre (A): 1.931000 1.047999 4.937500 number of atom coordinates read : 2988 total number of charged atoms : 2842 net assigned charge : 1.4009014E-02 assigned positive charge : 448.5726 centred at (gu) : 86.22617 87.03587 82.60855 assigned negative charge : -448.5594 centred at (gu) : 86.09106 86.97672 82.90381 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 86125 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26201 grid for indexing accessible points = 1.400000 m= 33155 mr = 60093 m= 6022 mr = 24332 m= 361 mr = 3761 m= 6 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 37369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 22375 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) : 0.6364986 object centre at (A) : 1.931000 1.047999 4.937500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4783076E-02 -2.9911965E-02 midg,1,midg; midg,igrid,midg 2.0734588E-02 1.3834506E-02 1,midg,midg; igrid,midg,midg -1.5961487E-02 -4.2221411E-03 gauss-seidel spectral radius is 0.9986786 estimated iterations to convergence 218 setup time was (sec) 0.8500000 now iterating at: 13:32:36 rms-change max change #iterations 4.697243 196.2693 at 10iterations 2.220123 72.74873 at 20iterations 1.050835 30.52831 at 30iterations 0.4990763 14.14632 at 40iterations 0.2361925 7.281369 at 50iterations 0.1124006 3.349134 at 60iterations 5.3561460E-02 1.637083 at 70iterations 2.5586443E-02 0.7804108 at 80iterations 1.2263105E-02 0.3926392 at 90iterations 5.9887744E-03 0.1917114 at 100iterations 3.0134593E-03 9.4158173E-02 at 110iterations 1.5958064E-03 5.0376892E-02 at 120iterations finished qdiffx linear iterations at : 13:32:42 total time elapsed so far: 6.820000 # loops : 120 mean,max change (kT/e) : 1.5958064E-03 5.0376892E-02 energy calculations done at 6.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 13:32:42 6.999u 0.171s 0:07.44 96.2% 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 13:32:42 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2988 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 350 has a net charge of -2.0000 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: 2.864244 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): -23.50200 27.36400 ymin,ymax (A): -25.14600 27.24200 zmin,zma (A): -23.02800 32.90300 x,y,z range (A): 50.86600 52.38800 55.93100 scale (grids/A): 2.864244 object centre (A): 1.931000 1.047999 4.937500 number of atom coordinates read : 2988 total number of charged atoms : 2842 net assigned charge : 1.4009014E-02 assigned positive charge : 448.5726 centred at (gu) : 84.33908 85.55384 78.91281 assigned negative charge : -448.5594 centred at (gu) : 84.13656 85.46507 79.35567 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 199180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26201 grid for indexing accessible points = 1.400000 m= 104295 mr = 145876 m= 40702 mr = 84914 m= 11075 mr = 32649 m= 1645 mr = 8199 m= 77 mr = 1032 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 84285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 22736 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) : 1.909496 object centre at (A) : 1.931000 1.047999 4.937500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4840726 -0.3425821 midg,1,midg; midg,igrid,midg 0.2364885 0.1318287 1,midg,midg; igrid,midg,midg -7.7117950E-02 6.5834881E-03 gauss-seidel spectral radius is 0.9992819 estimated iterations to convergence 294 setup time was (sec) 1.850000 now iterating at: 13:32:44 rms-change max change #iterations 10.99903 419.8143 at 10iterations 6.526334 148.3288 at 20iterations 3.857066 83.47084 at 30iterations 2.272015 50.54294 at 40iterations 1.334285 26.43427 at 50iterations 0.7801175 15.21397 at 60iterations 0.4568752 8.260811 at 70iterations 0.2661371 4.806218 at 80iterations 0.1552530 2.418120 at 90iterations 9.0436593E-02 1.683326 at 100iterations 5.2566487E-02 0.9038286 at 110iterations 3.0581599E-02 0.4768646 at 120iterations 1.7779989E-02 0.2996783 at 130iterations 1.0362737E-02 0.1809692 at 140iterations 6.0484014E-03 0.1000862 at 150iterations 3.5465586E-03 5.6036949E-02 at 160iterations 2.0960351E-03 3.6911011E-02 at 170iterations 1.2636263E-03 2.1671295E-02 at 180iterations finished qdiffx linear iterations at : 13:32:54 total time elapsed so far: 11.84000 # loops : 180 mean,max change (kT/e) : 1.2636263E-03 2.1671295E-02 energy calculations done at 11.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 13:32:55 12.014u 0.170s 0:12.45 97.8% 0+0k 0+0io 0pf+0w