Sun Oct 9 09:02:46 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 Sun Oct 9 2011 at 09:02:47 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5630 !!! WARNING: HIR 701 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5151879 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): 8.382999 77.48400 ymin,ymax (A): 2.532000 66.06100 zmin,zma (A): -14.81700 50.62400 x,y,z range (A): 69.10100 63.52900 65.44100 scale (grids/A): 0.5151879 object centre (A): 42.93350 34.29650 17.90350 number of atom coordinates read : 5630 total number of charged atoms : 5464 net assigned charge : 0.5140409 assigned positive charge : 850.4897 centred at (gu) : 90.26473 90.04305 88.93501 assigned negative charge : -849.9827 centred at (gu) : 90.11125 90.08755 88.95220 start vw surface at 0.2300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 9520 nv = 96 ne = 84 npr = 112631 no. pairs analyzed = 112631 no. exposed pairs = 7206 no. arc points = 50081 no. surface atoms = 2395 nbur = 3235 mkacc time = 0.3200000 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= 364 mr = 4881 m= 0 mr = 10 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 4993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4868 ## 683 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 12707 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.4538474E-11 -4.3427602E-11 midg,1,midg; midg,igrid,midg 1.7080987E-10 -1.6268990E-10 1,midg,midg; igrid,midg,midg -5.4080684E-10 6.1220795E-10 gauss-seidel spectral radius is 0.9807953 estimated iterations to convergence 60 setup time was (sec) 0.8900000 now iterating at: 09:02:48 rms-change max change #iterations 7.8189269E-02 10.90075 at 10iterations 4.7141928E-03 0.7071209 at 20iterations 4.9035432E-04 0.1048317 at 30iterations 1.2586737E-04 2.8896332E-02 at 40iterations 3.9965500E-05 8.7299347E-03 at 50iterations finished qdiffx linear iterations at : 09:02:51 total time elapsed so far: 4.180000 # loops : 50 mean,max change (kT/e) : 3.9965500E-05 8.7299347E-03 energy calculations done at 4.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.360000 DelPhi exited at 09:02:51 4.363u 0.272s 0:04.90 94.4% 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 Sun Oct 9 2011 at 09:02:51 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5630 !!! WARNING: HIR 701 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.545564 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): 8.382999 77.48400 ymin,ymax (A): 2.532000 66.06100 zmin,zma (A): -14.81700 50.62400 x,y,z range (A): 69.10100 63.52900 65.44100 scale (grids/A): 1.545564 object centre (A): 42.93350 34.29650 17.90350 number of atom coordinates read : 5630 total number of charged atoms : 5464 net assigned charge : 0.5140409 assigned positive charge : 850.4897 centred at (gu) : 90.79223 90.12734 86.80316 assigned negative charge : -849.9827 centred at (gu) : 90.33381 90.26273 86.85606 start vw surface at 0.2400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 107226 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50081 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 31510 mr = 73110 m= 2668 mr = 20603 m= 36 mr = 1077 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1450 time to turn everything in is 0.9500000 number of dielectric boundary points 46650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 667 ## 9 charges are in solution ## iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 41187 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) : 0.5151879 object centre at (A) : 42.93350 34.29650 17.90350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0605953E-02 -1.5431574E-02 midg,1,midg; midg,igrid,midg 1.4897637E-02 1.2430515E-03 1,midg,midg; igrid,midg,midg -1.8216459E-02 1.5185341E-02 gauss-seidel spectral radius is 0.9982337 estimated iterations to convergence 189 setup time was (sec) 1.260000 now iterating at: 09:02:53 rms-change max change #iterations 4.269242 145.7402 at 10iterations 1.798802 53.10791 at 20iterations 0.7577778 20.67913 at 30iterations 0.3203264 9.975294 at 40iterations 0.1352573 3.886536 at 50iterations 5.7145573E-02 1.635043 at 60iterations 2.4266774E-02 0.7034574 at 70iterations 1.0289582E-02 0.3182068 at 80iterations 4.3612365E-03 0.1324754 at 90iterations 1.8686285E-03 5.9070826E-02 at 100iterations 8.1143487E-04 2.5585175E-02 at 110iterations 3.6378592E-04 1.2971878E-02 at 120iterations finished qdiffx linear iterations at : 09:03:01 total time elapsed so far: 9.750000 # loops : 120 mean,max change (kT/e) : 3.6378592E-04 1.2971878E-02 energy calculations done at 9.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.930000 DelPhi exited at 09:03:02 9.932u 0.278s 0:10.53 96.8% 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 Sun Oct 9 2011 at 09:03:02 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5630 !!! WARNING: HIR 701 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.318346 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): 8.382999 77.48400 ymin,ymax (A): 2.532000 66.06100 zmin,zma (A): -14.81700 50.62400 x,y,z range (A): 69.10100 63.52900 65.44100 scale (grids/A): 2.318346 object centre (A): 42.93350 34.29650 17.90350 number of atom coordinates read : 5630 total number of charged atoms : 5464 net assigned charge : 0.5140409 assigned positive charge : 850.4897 centred at (gu) : 91.18810 90.19038 85.20400 assigned negative charge : -849.9827 centred at (gu) : 90.50065 90.39402 85.28407 start vw surface at 0.2400000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 249803 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50081 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 112344 mr = 180063 m= 28315 mr = 86686 m= 3812 mr = 20109 m= 202 mr = 2208 m= 0 mr = 53 time to grow re-entrant surface = 1.460000 no. cavity mid-points inaccessible to solvent = 5179 time to turn everything in is 2.330000 number of dielectric boundary points 105357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 2.500000 number of grid points assigned charge 43598 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) : 1.545564 object centre at (A) : 42.93350 34.29650 17.90350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3553291 -0.3798058 midg,1,midg; midg,igrid,midg 0.3057267 -2.7433515E-03 1,midg,midg; igrid,midg,midg -0.4353463 0.1524552 gauss-seidel spectral radius is 0.9992265 estimated iterations to convergence 284 setup time was (sec) 2.680000 now iterating at: 09:03:05 rms-change max change #iterations 11.58992 278.4166 at 10iterations 6.862029 171.1432 at 20iterations 4.032451 82.45975 at 30iterations 2.350205 49.03099 at 40iterations 1.365729 26.68312 at 50iterations 0.7906140 16.97986 at 60iterations 0.4553760 8.915470 at 70iterations 0.2619821 4.838459 at 80iterations 0.1506055 2.773972 at 90iterations 8.6626381E-02 1.785175 at 100iterations 4.9600620E-02 1.075218 at 110iterations 2.8394857E-02 0.5623894 at 120iterations 1.6249320E-02 0.2773838 at 130iterations 9.3196724E-03 0.1814384 at 140iterations 5.3258534E-03 9.7139359E-02 at 150iterations 3.0516372E-03 5.4053307E-02 at 160iterations 1.7537163E-03 2.7925134E-02 at 170iterations 1.0155714E-03 1.7933607E-02 at 180iterations finished qdiffx linear iterations at : 09:03:19 total time elapsed so far: 17.12000 # loops : 180 mean,max change (kT/e) : 1.0155714E-03 1.7933607E-02 energy calculations done at 17.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.30000 DelPhi exited at 09:03:20 17.304u 0.314s 0:17.90 98.3% 0+0k 0+0io 0pf+0w