Mon Oct 10 14:04:02 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 Mon Oct 10 2011 at 14:04:02 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7502635 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): -20.74800 24.27700 ymin,ymax (A): -35.63600 8.097000 zmin,zma (A): -43.90900 3.541000 x,y,z range (A): 45.02500 43.73300 47.45000 scale (grids/A): 0.7502635 object centre (A): 1.764501 -13.76950 -20.18400 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 318.4519 centred at (gu) : 88.94590 89.28646 89.70429 assigned negative charge : -324.4520 centred at (gu) : 88.98415 89.21457 89.51772 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8185 nv = 96 ne = 84 npr = 44171 no. pairs analyzed = 44171 no. exposed pairs = 2694 no. arc points = 18653 no. surface atoms = 911 nbur = 1204 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 603 mr = 4583 m= 6 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.1800000 number of dielectric boundary points 4101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1525 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8594 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9134602E-07 9.5508277E-08 midg,1,midg; midg,igrid,midg -2.5283606E-07 -3.5946151E-08 1,midg,midg; igrid,midg,midg -9.8400811E-08 -1.4795008E-07 gauss-seidel spectral radius is 0.9907402 estimated iterations to convergence 84 setup time was (sec) 0.3600000 now iterating at: 14:04:02 rms-change max change #iterations 0.2628363 31.39289 at 10iterations 3.5674766E-02 4.489236 at 20iterations 4.9729859E-03 0.5998039 at 30iterations 6.8253628E-04 7.9277039E-02 at 40iterations 9.6165619E-05 1.2475014E-02 at 50iterations finished qdiffx linear iterations at : 14:04:05 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 9.6165619E-05 1.2475014E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 14:04:06 3.407u 0.193s 0:04.05 88.6% 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 Mon Oct 10 2011 at 14:04:06 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.250790 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): -20.74800 24.27700 ymin,ymax (A): -35.63600 8.097000 zmin,zma (A): -43.90900 3.541000 x,y,z range (A): 45.02500 43.73300 47.45000 scale (grids/A): 2.250790 object centre (A): 1.764501 -13.76950 -20.18400 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 318.4519 centred at (gu) : 86.83784 87.85926 89.11294 assigned negative charge : -324.4520 centred at (gu) : 86.95233 87.64372 88.55298 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 85705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18653 grid for indexing accessible points = 1.400000 m= 33916 mr = 59317 m= 7450 mr = 25682 m= 884 mr = 5208 m= 31 mr = 483 m= 0 mr = 5 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 380 time to turn everything in is 0.4200000 number of dielectric boundary points 37291 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 15759 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) : 0.7502635 object centre at (A) : 1.764501 -13.76950 -20.18400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1555181 -5.4153935E-03 midg,1,midg; midg,igrid,midg -3.6103752E-02 -2.2938708E-02 1,midg,midg; igrid,midg,midg -1.1253493E-02 -9.6837645E-03 gauss-seidel spectral radius is 0.9989492 estimated iterations to convergence 244 setup time was (sec) 0.6500000 now iterating at: 14:04:07 rms-change max change #iterations 5.241336 211.1164 at 10iterations 2.671434 86.81744 at 20iterations 1.374276 39.15719 at 30iterations 0.7054057 20.72397 at 40iterations 0.3624242 10.31543 at 50iterations 0.1864299 5.277686 at 60iterations 9.5230542E-02 2.683517 at 70iterations 4.9115568E-02 1.334818 at 80iterations 2.5090342E-02 0.6851463 at 90iterations 1.2925414E-02 0.3508902 at 100iterations 6.6386769E-03 0.1879005 at 110iterations 3.4166921E-03 9.3816757E-02 at 120iterations finished qdiffx linear iterations at : 14:04:14 total time elapsed so far: 7.910000 # loops : 120 mean,max change (kT/e) : 3.4166921E-03 9.3816757E-02 energy calculations done at 7.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 14:04:15 8.046u 0.205s 0:08.61 95.7% 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 Mon Oct 10 2011 at 14:04:15 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.376185 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): -20.74800 24.27700 ymin,ymax (A): -35.63600 8.097000 zmin,zma (A): -43.90900 3.541000 x,y,z range (A): 45.02500 43.73300 47.45000 scale (grids/A): 3.376185 object centre (A): 1.764501 -13.76950 -20.18400 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 318.4519 centred at (gu) : 85.25671 86.78881 88.66923 assigned negative charge : -324.4520 centred at (gu) : 85.42850 86.46559 87.82948 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 197426 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18653 grid for indexing accessible points = 1.400000 m= 104434 mr = 143058 m= 44508 mr = 86447 m= 14320 mr = 36781 m= 3455 mr = 11414 m= 463 mr = 2626 m= 26 mr = 288 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 1325 time to turn everything in is 1.330000 number of dielectric boundary points 84012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 15804 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) : 2.250790 object centre at (A) : 1.764501 -13.76950 -20.18400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.504719 6.1909221E-02 midg,1,midg; midg,igrid,midg -0.1744321 -0.2109343 1,midg,midg; igrid,midg,midg -0.1858682 -0.1493124 gauss-seidel spectral radius is 0.9993256 estimated iterations to convergence 304 setup time was (sec) 1.570000 now iterating at: 14:04:16 rms-change max change #iterations 11.25160 314.1600 at 10iterations 6.624053 127.6189 at 20iterations 3.916185 82.20785 at 30iterations 2.307293 42.60827 at 40iterations 1.364200 22.56491 at 50iterations 0.8036269 13.89101 at 60iterations 0.4733822 7.683922 at 70iterations 0.2791035 4.464256 at 80iterations 0.1640978 2.644577 at 90iterations 9.6575513E-02 1.518850 at 100iterations 5.6885380E-02 0.8842068 at 110iterations 3.3475220E-02 0.6048284 at 120iterations 1.9725354E-02 0.3096008 at 130iterations 1.1592303E-02 0.1947584 at 140iterations 6.8338905E-03 0.1081934 at 150iterations 4.0285853E-03 6.2720776E-02 at 160iterations 2.3714334E-03 4.4602394E-02 at 170iterations 1.3963598E-03 2.3665428E-02 at 180iterations finished qdiffx linear iterations at : 14:04:28 total time elapsed so far: 13.48000 # loops : 180 mean,max change (kT/e) : 1.3963598E-03 2.3665428E-02 energy calculations done at 13.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.61000 DelPhi exited at 14:04:29 13.616u 0.239s 0:14.22 97.3% 0+0k 0+0io 0pf+0w