Tue Oct 11 08:33:47 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 08:33:47 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 = 2108 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7187853 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): -8.488000 38.40700 ymin,ymax (A): -30.12200 19.40600 zmin,zma (A): 3.758000 46.38800 x,y,z range (A): 46.89500 49.52800 42.63000 scale (grids/A): 0.7187853 object centre (A): 14.95950 -5.358000 25.07300 number of atom coordinates read : 2108 total number of charged atoms : 1978 net assigned charge : 6.039011 assigned positive charge : 324.7460 centred at (gu) : 90.63718 89.28733 90.30339 assigned negative charge : -318.7071 centred at (gu) : 90.51287 89.33826 90.41230 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7467 nv = 96 ne = 84 npr = 42175 no. pairs analyzed = 42175 no. exposed pairs = 2493 no. arc points = 17149 no. surface atoms = 855 nbur = 1253 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 518 mr = 4417 m= 0 mr = 88 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1523 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8107 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2798391E-07 -6.0933858E-09 midg,1,midg; midg,igrid,midg 1.1292208E-07 2.8886173E-08 1,midg,midg; igrid,midg,midg -1.3410730E-08 1.6430394E-07 gauss-seidel spectral radius is 0.9899105 estimated iterations to convergence 81 setup time was (sec) 0.6400000 now iterating at: 08:33:48 rms-change max change #iterations 0.2183768 39.50844 at 10iterations 2.8870614E-02 3.610205 at 20iterations 3.8442533E-03 0.5473726 at 30iterations 6.3864293E-04 8.8760376E-02 at 40iterations 1.6277135E-04 2.0805359E-02 at 50iterations finished qdiffx linear iterations at : 08:33:52 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 1.6277135E-04 2.0805359E-02 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.680000 DelPhi exited at 08:33:53 4.686u 0.426s 0:05.43 93.9% 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 08:33:53 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 = 2108 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.156356 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): -8.488000 38.40700 ymin,ymax (A): -30.12200 19.40600 zmin,zma (A): 3.758000 46.38800 x,y,z range (A): 46.89500 49.52800 42.63000 scale (grids/A): 2.156356 object centre (A): 14.95950 -5.358000 25.07300 number of atom coordinates read : 2108 total number of charged atoms : 1978 net assigned charge : 6.039011 assigned positive charge : 324.7460 centred at (gu) : 91.91163 87.86202 90.90991 assigned negative charge : -318.7071 centred at (gu) : 91.53888 88.01484 91.23709 start vw surface at 0.1600000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 79227 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17149 grid for indexing accessible points = 1.400000 m= 32902 mr = 57065 m= 6566 mr = 25423 m= 580 mr = 4431 m= 18 mr = 293 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8400000 number of dielectric boundary points 32081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 15727 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) : 0.7187853 object centre at (A) : 14.95950 -5.358000 25.07300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6106378E-02 2.0554338E-02 midg,1,midg; midg,igrid,midg 4.2444922E-02 3.4233861E-02 1,midg,midg; igrid,midg,midg -4.4708792E-02 3.4720037E-02 gauss-seidel spectral radius is 0.9988652 estimated iterations to convergence 235 setup time was (sec) 1.190000 now iterating at: 08:33:55 rms-change max change #iterations 4.844686 196.3739 at 10iterations 2.411763 86.13457 at 20iterations 1.214175 39.02962 at 30iterations 0.6085556 18.62028 at 40iterations 0.3055532 9.096972 at 50iterations 0.1530216 4.365771 at 60iterations 7.6952964E-02 2.135269 at 70iterations 3.8749311E-02 1.066168 at 80iterations 1.9568224E-02 0.5858307 at 90iterations 9.9645304E-03 0.3169546 at 100iterations 5.1018684E-03 0.1726799 at 110iterations 2.6704785E-03 7.9833984E-02 at 120iterations finished qdiffx linear iterations at : 08:34:04 total time elapsed so far: 11.09000 # loops : 120 mean,max change (kT/e) : 2.6704785E-03 7.9833984E-02 energy calculations done at 11.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.32000 DelPhi exited at 08:34:05 11.327u 0.459s 0:12.09 97.3% 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 08:34:05 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 = 2108 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.234534 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): -8.488000 38.40700 ymin,ymax (A): -30.12200 19.40600 zmin,zma (A): 3.758000 46.38800 x,y,z range (A): 46.89500 49.52800 42.63000 scale (grids/A): 3.234534 object centre (A): 14.95950 -5.358000 25.07300 number of atom coordinates read : 2108 total number of charged atoms : 1978 net assigned charge : 6.039011 assigned positive charge : 324.7460 centred at (gu) : 92.86736 86.79309 91.36490 assigned negative charge : -318.7071 centred at (gu) : 92.30823 87.02225 91.85563 start vw surface at 0.1300000 fill in re-entrant regions at 1.030000 boundary points on vw surface= 182552 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17149 grid for indexing accessible points = 1.400000 m= 101734 mr = 137063 m= 42782 mr = 85539 m= 12426 mr = 35586 m= 2416 mr = 9800 m= 304 mr = 1720 m= 9 mr = 176 m= 0 mr = 0 time to grow re-entrant surface = 1.430000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.620000 number of dielectric boundary points 72339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.770000 number of grid points assigned charge 15824 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) : 2.156356 object centre at (A) : 14.95950 -5.358000 25.07300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1289681 0.1598274 midg,1,midg; midg,igrid,midg 0.2877535 0.2065363 1,midg,midg; igrid,midg,midg -0.4832937 0.2916438 gauss-seidel spectral radius is 0.9993051 estimated iterations to convergence 299 setup time was (sec) 2.980000 now iterating at: 08:34:09 rms-change max change #iterations 10.72874 455.5802 at 10iterations 6.359554 151.8546 at 20iterations 3.775786 77.40527 at 30iterations 2.239820 47.41071 at 40iterations 1.322905 25.60818 at 50iterations 0.7792304 13.32434 at 60iterations 0.4601097 7.591633 at 70iterations 0.2710730 4.875803 at 80iterations 0.1595345 2.985786 at 90iterations 9.3970895E-02 1.660477 at 100iterations 5.5353843E-02 0.9705887 at 110iterations 3.2814756E-02 0.5272903 at 120iterations 1.9559832E-02 0.3693504 at 130iterations 1.1822878E-02 0.2248363 at 140iterations 7.3410366E-03 0.1346970 at 150iterations 4.7219046E-03 8.7293625E-02 at 160iterations 3.2047546E-03 5.9204102E-02 at 170iterations 2.3143806E-03 4.1450500E-02 at 180iterations finished qdiffx linear iterations at : 08:34:28 total time elapsed so far: 22.74000 # loops : 180 mean,max change (kT/e) : 2.3143806E-03 4.1450500E-02 energy calculations done at 22.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.96000 DelPhi exited at 08:34:29 22.960u 0.516s 0:23.78 98.6% 0+0k 0+0io 0pf+0w