Tue Oct 11 03:14:51 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 03:14:51 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3210 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: 0.5570072 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): -24.12100 33.31400 ymin,ymax (A): -39.01700 22.46100 zmin,zma (A): -31.65100 32.26200 x,y,z range (A): 57.43500 61.47800 63.91300 scale (grids/A): 0.5570072 object centre (A): 4.596499 -8.277999 0.3055000 number of atom coordinates read : 3210 total number of charged atoms : 3055 net assigned charge : -4.999985 assigned positive charge : 479.5609 centred at (gu) : 90.14727 91.37257 91.92400 assigned negative charge : -484.5623 centred at (gu) : 90.21171 91.27769 91.95271 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6573 nv = 96 ne = 84 npr = 62894 no. pairs analyzed = 62894 no. exposed pairs = 4458 no. arc points = 30838 no. surface atoms = 1497 nbur = 1713 mkacc time = 0.1800000 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 = 1.540000 m= 276 mr = 3201 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3055 ## 377 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8490 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1348089E-10 -1.2613581E-09 midg,1,midg; midg,igrid,midg -1.0868519E-09 7.5885170E-10 1,midg,midg; igrid,midg,midg 2.0144596E-10 -1.2227093E-09 gauss-seidel spectral radius is 0.9834030 estimated iterations to convergence 64 setup time was (sec) 0.6700000 now iterating at: 03:14:52 rms-change max change #iterations 8.4509283E-02 13.80264 at 10iterations 5.9929178E-03 1.085419 at 20iterations 4.3459726E-04 7.0886612E-02 at 30iterations 4.2689262E-05 8.6050034E-03 at 40iterations 7.3424317E-06 1.8348694E-03 at 50iterations finished qdiffx linear iterations at : 03:14:55 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 7.3424317E-06 1.8348694E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 03:14:56 4.230u 0.275s 0:04.91 91.6% 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 03:14:56 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3210 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: 1.671021 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): -24.12100 33.31400 ymin,ymax (A): -39.01700 22.46100 zmin,zma (A): -31.65100 32.26200 x,y,z range (A): 57.43500 61.47800 63.91300 scale (grids/A): 1.671021 object centre (A): 4.596499 -8.277999 0.3055000 number of atom coordinates read : 3210 total number of charged atoms : 3055 net assigned charge : -4.999985 assigned positive charge : 479.5609 centred at (gu) : 90.44118 94.11694 95.77155 assigned negative charge : -484.5623 centred at (gu) : 90.63488 93.83276 95.85781 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 72795 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30838 grid for indexing accessible points = 1.400000 m= 21712 mr = 47809 m= 2065 mr = 14195 m= 55 mr = 834 m= 0 mr = 1 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 33788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 285 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 23499 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) : 0.5570072 object centre at (A) : 4.596499 -8.277999 0.3055000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9575922E-02 -9.4137108E-03 midg,1,midg; midg,igrid,midg -2.4229873E-02 -1.2988575E-02 1,midg,midg; igrid,midg,midg 8.4718214E-03 -9.7378278E-03 gauss-seidel spectral radius is 0.9983008 estimated iterations to convergence 193 setup time was (sec) 0.9500000 now iterating at: 03:14:57 rms-change max change #iterations 3.709440 161.6116 at 10iterations 1.570353 66.30791 at 20iterations 0.6726154 22.43239 at 30iterations 0.2869735 11.18420 at 40iterations 0.1236175 4.570155 at 50iterations 5.2888811E-02 1.838660 at 60iterations 2.2658680E-02 0.8039725 at 70iterations 9.6928142E-03 0.3612726 at 80iterations 4.1605034E-03 0.1520996 at 90iterations 1.7805388E-03 5.9784889E-02 at 100iterations 7.6703524E-04 2.5607824E-02 at 110iterations 3.3114187E-04 1.0878563E-02 at 120iterations finished qdiffx linear iterations at : 03:15:06 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 3.3114187E-04 1.0878563E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.620000 DelPhi exited at 03:15:06 9.623u 0.322s 0:10.34 96.1% 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 03:15:06 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3210 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.506532 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): -24.12100 33.31400 ymin,ymax (A): -39.01700 22.46100 zmin,zma (A): -31.65100 32.26200 x,y,z range (A): 57.43500 61.47800 63.91300 scale (grids/A): 2.506532 object centre (A): 4.596499 -8.277999 0.3055000 number of atom coordinates read : 3210 total number of charged atoms : 3055 net assigned charge : -4.999985 assigned positive charge : 479.5609 centred at (gu) : 90.66171 96.17519 98.65708 assigned negative charge : -484.5623 centred at (gu) : 90.95222 95.74912 98.78681 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 169022 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30838 grid for indexing accessible points = 1.400000 m= 75403 mr = 117525 m= 20570 mr = 57941 m= 3018 mr = 14750 m= 208 mr = 1740 m= 2 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.590000 number of dielectric boundary points 76189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 24425 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) : 1.671021 object centre at (A) : 4.596499 -8.277999 0.3055000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4734810 -9.7357653E-02 midg,1,midg; midg,igrid,midg -0.4616094 -0.2850977 1,midg,midg; igrid,midg,midg 0.1019002 -0.1211994 gauss-seidel spectral radius is 0.9991878 estimated iterations to convergence 277 setup time was (sec) 1.940000 now iterating at: 03:15:09 rms-change max change #iterations 9.524339 402.5076 at 10iterations 5.477716 125.7843 at 20iterations 3.128721 67.60485 at 30iterations 1.777134 40.26656 at 40iterations 1.006017 21.00002 at 50iterations 0.5658218 11.83081 at 60iterations 0.3186815 6.585125 at 70iterations 0.1791039 4.432412 at 80iterations 0.1004650 2.290438 at 90iterations 5.6262605E-02 1.058196 at 100iterations 3.1541817E-02 0.6223793 at 110iterations 1.7650405E-02 0.3750687 at 120iterations 9.8789297E-03 0.1876230 at 130iterations 5.5269185E-03 0.1061025 at 140iterations 3.0933397E-03 6.4094543E-02 at 150iterations 1.7295271E-03 3.7363052E-02 at 160iterations 9.6680818E-04 2.0081520E-02 at 170iterations 5.4107269E-04 9.6664429E-03 at 180iterations finished qdiffx linear iterations at : 03:15:23 total time elapsed so far: 16.08000 # loops : 180 mean,max change (kT/e) : 5.4107269E-04 9.6664429E-03 energy calculations done at 16.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.26000 DelPhi exited at 03:15:23 16.257u 0.332s 0:16.95 97.8% 0+0k 0+0io 0pf+0w