Mon Oct 10 23:38:04 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+sph.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 = amb.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 23:38:04 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1850 !!! WARNING: no radius record for F1 F1 2 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: 0.6585397 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): -13.89300 24.59000 ymin,ymax (A): -25.38200 16.49000 zmin,zma (A): -7.854000 46.20500 x,y,z range (A): 38.48300 41.87200 54.05900 scale (grids/A): 0.6585397 object centre (A): 5.348500 -4.446000 19.17550 number of atom coordinates read : 1850 total number of charged atoms : 1704 net assigned charge : 6.000022 assigned positive charge : 268.3192 centred at (gu) : 90.23521 90.27175 91.63417 assigned negative charge : -262.3193 centred at (gu) : 90.11243 90.27583 91.37041 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5183 nv = 96 ne = 84 npr = 38821 no. pairs analyzed = 38821 no. exposed pairs = 2244 no. arc points = 15577 no. surface atoms = 766 nbur = 1084 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 283 mr = 2786 m= 0 mr = 36 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3200000 number of dielectric boundary points 2644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1454 ## 116 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6097 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4577187E-08 6.6365999E-08 midg,1,midg; midg,igrid,midg 1.3772898E-08 1.4249907E-08 1,midg,midg; igrid,midg,midg -1.8408594E-09 3.1082546E-08 gauss-seidel spectral radius is 0.9879762 estimated iterations to convergence 74 setup time was (sec) 0.6000000 now iterating at: 23:38:05 rms-change max change #iterations 0.1361233 20.86805 at 10iterations 1.4367962E-02 2.308937 at 20iterations 1.5603752E-03 0.2409668 at 30iterations 1.8469157E-04 3.4252167E-02 at 40iterations 2.1323975E-05 3.9463043E-03 at 50iterations finished qdiffx linear iterations at : 23:38:08 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 2.1323975E-05 3.9463043E-03 energy calculations done at 3.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 23:38:09 4.027u 0.189s 0:04.77 88.0% 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 Mon Oct 10 2011 at 23:38:09 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1850 !!! WARNING: no radius record for F1 F1 2 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: 1.975619 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): -13.89300 24.59000 ymin,ymax (A): -25.38200 16.49000 zmin,zma (A): -7.854000 46.20500 x,y,z range (A): 38.48300 41.87200 54.05900 scale (grids/A): 1.975619 object centre (A): 5.348500 -4.446000 19.17550 number of atom coordinates read : 1850 total number of charged atoms : 1704 net assigned charge : 6.000022 assigned positive charge : 268.3192 centred at (gu) : 90.70573 90.81529 94.90298 assigned negative charge : -262.3193 centred at (gu) : 90.33752 90.82795 94.11144 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 55926 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15577 grid for indexing accessible points = 1.400000 m= 19627 mr = 38421 m= 3244 mr = 14218 m= 167 mr = 2016 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1799 time to turn everything in is 0.5600000 number of dielectric boundary points 24278 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 13459 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) : 0.6585397 object centre at (A) : 5.348500 -4.446000 19.17550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2930807E-03 9.9142529E-02 midg,1,midg; midg,igrid,midg -2.6777040E-03 2.7786277E-02 1,midg,midg; igrid,midg,midg 1.7009529E-03 1.2936437E-02 gauss-seidel spectral radius is 0.9986438 estimated iterations to convergence 215 setup time was (sec) 0.9000000 now iterating at: 23:38:10 rms-change max change #iterations 3.687860 169.2091 at 10iterations 1.730616 72.84008 at 20iterations 0.8127723 28.38708 at 30iterations 0.3814413 13.22920 at 40iterations 0.1787951 6.140862 at 50iterations 8.3610967E-02 3.462589 at 60iterations 3.9263297E-02 1.345406 at 70iterations 1.8439550E-02 0.6497917 at 80iterations 8.7002814E-03 0.2874889 at 90iterations 4.1010482E-03 0.1411133 at 100iterations 1.9424869E-03 6.7214966E-02 at 110iterations 9.2370925E-04 3.1738281E-02 at 120iterations finished qdiffx linear iterations at : 23:38:18 total time elapsed so far: 8.470000 # loops : 120 mean,max change (kT/e) : 9.2370925E-04 3.1738281E-02 energy calculations done at 8.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.740000 DelPhi exited at 23:38:20 8.739u 0.188s 0:10.48 85.0% 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 Mon Oct 10 2011 at 23:38:20 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1850 !!! WARNING: no radius record for F1 F1 2 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: 2.963429 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): -13.89300 24.59000 ymin,ymax (A): -25.38200 16.49000 zmin,zma (A): -7.854000 46.20500 x,y,z range (A): 38.48300 41.87200 54.05900 scale (grids/A): 2.963429 object centre (A): 5.348500 -4.446000 19.17550 number of atom coordinates read : 1850 total number of charged atoms : 1704 net assigned charge : 6.000022 assigned positive charge : 268.3192 centred at (gu) : 91.05863 91.22316 97.35436 assigned negative charge : -262.3193 centred at (gu) : 90.50629 91.24200 96.16715 start vw surface at 0.1900000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 129637 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15577 grid for indexing accessible points = 1.400000 m= 63148 mr = 93310 m= 23029 mr = 51184 m= 5840 mr = 18284 m= 830 mr = 4429 m= 24 mr = 497 m= 0 mr = 7 time to grow re-entrant surface = 0.7400001 no. cavity mid-points inaccessible to solvent = 6188 time to turn everything in is 1.350000 number of dielectric boundary points 54797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 13632 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) : 1.975619 object centre at (A) : 5.348500 -4.446000 19.17550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3821422E-02 1.002343 midg,1,midg; midg,igrid,midg -6.7835256E-02 0.3301800 1,midg,midg; igrid,midg,midg 2.6336543E-02 8.9200057E-02 gauss-seidel spectral radius is 0.9992419 estimated iterations to convergence 287 setup time was (sec) 1.700000 now iterating at: 23:38:22 rms-change max change #iterations 8.472030 312.5449 at 10iterations 4.872499 109.8817 at 20iterations 2.802358 68.68646 at 30iterations 1.604268 37.80154 at 40iterations 0.9178801 19.43810 at 50iterations 0.5247543 11.83833 at 60iterations 0.2998241 6.536713 at 70iterations 0.1708921 3.474404 at 80iterations 9.7847126E-02 2.062036 at 90iterations 5.5922873E-02 1.303253 at 100iterations 3.1884305E-02 0.6902466 at 110iterations 1.8278543E-02 0.3843002 at 120iterations 1.0431360E-02 0.2229414 at 130iterations 5.9915497E-03 0.1198254 at 140iterations 3.4451052E-03 6.7876816E-02 at 150iterations 1.9955018E-03 4.1353226E-02 at 160iterations 1.1732588E-03 2.7671814E-02 at 170iterations 7.0330047E-04 1.7204285E-02 at 180iterations finished qdiffx linear iterations at : 23:38:34 total time elapsed so far: 13.66000 # loops : 180 mean,max change (kT/e) : 7.0330047E-04 1.7204285E-02 energy calculations done at 13.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.91000 DelPhi exited at 23:38:35 13.910u 0.182s 0:14.76 95.4% 0+0k 0+0io 0pf+0w