Mon Oct 10 17:05:12 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 17:05:12 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4826 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5122523 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): -18.32300 36.68700 ymin,ymax (A): -30.84500 35.59700 zmin,zma (A): -4.065000 65.43200 x,y,z range (A): 55.01000 66.44200 69.49700 scale (grids/A): 0.5122523 object centre (A): 9.182000 2.375999 30.68350 number of atom coordinates read : 4826 total number of charged atoms : 4575 net assigned charge : 7.706038 assigned positive charge : 726.0344 centred at (gu) : 90.35744 90.30699 88.49269 assigned negative charge : -718.3328 centred at (gu) : 90.23996 90.33927 88.46391 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8045 nv = 96 ne = 84 npr = 97265 no. pairs analyzed = 97265 no. exposed pairs = 6185 no. arc points = 42749 no. surface atoms = 2076 nbur = 2750 mkacc time = 0.2300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 286 mr = 4093 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4187 ## 612 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 10711 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2783011E-11 1.3428134E-10 midg,1,midg; midg,igrid,midg 1.9176312E-10 2.9293155E-11 1,midg,midg; igrid,midg,midg -1.9527510E-10 4.8454152E-10 gauss-seidel spectral radius is 0.9805158 estimated iterations to convergence 59 setup time was (sec) 0.7500000 now iterating at: 17:05:13 rms-change max change #iterations 6.9746993E-02 9.554150 at 10iterations 4.6500694E-03 0.9234619 at 20iterations 8.2906656E-04 0.1384354 at 30iterations 2.8544260E-04 3.4896851E-02 at 40iterations 1.1266469E-04 1.4138222E-02 at 50iterations finished qdiffx linear iterations at : 17:05:16 total time elapsed so far: 3.590000 # loops : 50 mean,max change (kT/e) : 1.1266469E-04 1.4138222E-02 energy calculations done at 3.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.790000 DelPhi exited at 17:05:17 3.790u 0.184s 0:04.80 82.7% 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 17:05:17 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4826 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.536757 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): -18.32300 36.68700 ymin,ymax (A): -30.84500 35.59700 zmin,zma (A): -4.065000 65.43200 x,y,z range (A): 55.01000 66.44200 69.49700 scale (grids/A): 1.536757 object centre (A): 9.182000 2.375999 30.68350 number of atom coordinates read : 4826 total number of charged atoms : 4575 net assigned charge : 7.706038 assigned positive charge : 726.0344 centred at (gu) : 91.07095 90.91980 85.47672 assigned negative charge : -718.3328 centred at (gu) : 90.71985 91.01719 85.39180 start vw surface at 0.2300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 91426 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42749 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26365 mr = 62576 m= 2186 mr = 17051 m= 51 mr = 863 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 39538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 496 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 34339 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) : 0.5122523 object centre at (A) : 9.182000 2.375999 30.68350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0836476E-03 1.8962763E-02 midg,1,midg; midg,igrid,midg 1.8420998E-03 -9.6214013E-03 1,midg,midg; igrid,midg,midg 2.8488593E-04 1.4225782E-02 gauss-seidel spectral radius is 0.9981362 estimated iterations to convergence 184 setup time was (sec) 1.050000 now iterating at: 17:05:18 rms-change max change #iterations 3.840150 150.6280 at 10iterations 1.576612 50.14575 at 20iterations 0.6513702 19.96546 at 30iterations 0.2690502 8.979985 at 40iterations 0.1107709 3.378484 at 50iterations 4.5915402E-02 1.384521 at 60iterations 1.9061349E-02 0.6040850 at 70iterations 7.9453560E-03 0.2567005 at 80iterations 3.3377567E-03 0.1017723 at 90iterations 1.4467307E-03 5.0220490E-02 at 100iterations 6.6159910E-04 2.0383835E-02 at 110iterations 3.3967118E-04 1.0566711E-02 at 120iterations finished qdiffx linear iterations at : 17:05:26 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 3.3967118E-04 1.0566711E-02 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.440000 DelPhi exited at 17:05:27 8.447u 0.214s 0:09.43 91.7% 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 17:05:27 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4826 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 2.305135 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): -18.32300 36.68700 ymin,ymax (A): -30.84500 35.59700 zmin,zma (A): -4.065000 65.43200 x,y,z range (A): 55.01000 66.44200 69.49700 scale (grids/A): 2.305135 object centre (A): 9.182000 2.375999 30.68350 number of atom coordinates read : 4826 total number of charged atoms : 4575 net assigned charge : 7.706038 assigned positive charge : 726.0344 centred at (gu) : 91.60613 91.37940 83.21480 assigned negative charge : -718.3328 centred at (gu) : 91.07950 91.52587 83.08761 start vw surface at 0.2600000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 213184 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42749 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 95131 mr = 154166 m= 23265 mr = 73482 m= 3091 mr = 16066 m= 175 mr = 1681 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.740000 number of dielectric boundary points 89404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 75 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 36488 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) : 1.536757 object centre at (A) : 9.182000 2.375999 30.68350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1449905 0.4831312 midg,1,midg; midg,igrid,midg -0.1067268 -0.2544864 1,midg,midg; igrid,midg,midg -2.3922932E-03 0.2213658 gauss-seidel spectral radius is 0.9991738 estimated iterations to convergence 275 setup time was (sec) 2.060000 now iterating at: 17:05:29 rms-change max change #iterations 10.48813 249.7684 at 10iterations 6.080450 170.5271 at 20iterations 3.491603 101.9341 at 30iterations 1.991408 43.28889 at 40iterations 1.130051 27.22497 at 50iterations 0.6391735 14.81661 at 60iterations 0.3596902 9.852770 at 70iterations 0.2020100 4.116617 at 80iterations 0.1135809 2.160269 at 90iterations 6.3538305E-02 1.244940 at 100iterations 3.5615988E-02 0.6799450 at 110iterations 1.9936481E-02 0.4133725 at 120iterations 1.1136920E-02 0.2227459 at 130iterations 6.2468559E-03 0.1191454 at 140iterations 3.4890636E-03 6.4258575E-02 at 150iterations 1.9534477E-03 3.7554741E-02 at 160iterations 1.0961820E-03 2.0316362E-02 at 170iterations 6.1690842E-04 1.2417793E-02 at 180iterations finished qdiffx linear iterations at : 17:05:39 total time elapsed so far: 12.50000 # loops : 180 mean,max change (kT/e) : 6.1690842E-04 1.2417793E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 17:05:40 12.692u 0.247s 0:13.37 96.7% 0+0k 0+0io 0pf+0w