Tue Oct 11 08:07:09 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 Tue Oct 11 2011 at 08:07:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 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: 0.5648821 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): -18.92100 25.52800 ymin,ymax (A): 16.84900 79.87100 zmin,zma (A): 2.529000 52.24700 x,y,z range (A): 44.44900 63.02200 49.71800 scale (grids/A): 0.5648821 object centre (A): 3.303500 48.36000 27.38800 number of atom coordinates read : 2382 total number of charged atoms : 2245 net assigned charge : 9.000023 assigned positive charge : 359.1702 centred at (gu) : 90.20716 88.53902 91.52908 assigned negative charge : -350.1709 centred at (gu) : 90.08379 88.63741 91.51167 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5044 nv = 96 ne = 84 npr = 47243 no. pairs analyzed = 47243 no. exposed pairs = 3107 no. arc points = 22167 no. surface atoms = 1037 nbur = 1345 mkacc time = 0.1300000 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 = 1.512000 m= 210 mr = 2569 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2264 ## 307 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 6426 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6293770E-10 1.8626949E-09 midg,1,midg; midg,igrid,midg 3.0134042E-09 7.8223338E-11 1,midg,midg; igrid,midg,midg -1.6195852E-10 2.4936395E-09 gauss-seidel spectral radius is 0.9837869 estimated iterations to convergence 65 setup time was (sec) 0.5900000 now iterating at: 08:07:10 rms-change max change #iterations 7.3761664E-02 11.41693 at 10iterations 5.5170418E-03 0.8544623 at 20iterations 4.2009162E-04 6.6288710E-02 at 30iterations 5.4117001E-05 1.3708115E-02 at 40iterations 1.3572956E-05 3.7794113E-03 at 50iterations finished qdiffx linear iterations at : 08:07:13 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 1.3572956E-05 3.7794113E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 08:07:14 4.123u 0.280s 0:04.96 88.7% 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 Tue Oct 11 2011 at 08:07:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 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: 1.694646 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): -18.92100 25.52800 ymin,ymax (A): 16.84900 79.87100 zmin,zma (A): 2.529000 52.24700 x,y,z range (A): 44.44900 63.02200 49.71800 scale (grids/A): 1.694646 object centre (A): 3.303500 48.36000 27.38800 number of atom coordinates read : 2382 total number of charged atoms : 2245 net assigned charge : 9.000023 assigned positive charge : 359.1702 centred at (gu) : 90.62113 85.61678 94.58665 assigned negative charge : -350.1709 centred at (gu) : 90.25127 85.91209 94.53487 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 55453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22167 grid for indexing accessible points = 1.400000 m= 17662 mr = 36946 m= 2002 mr = 12256 m= 61 mr = 1053 m= 0 mr = 6 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 89 time to turn everything in is 0.5200000 number of dielectric boundary points 24917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17340 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) : 0.5648821 object centre at (A) : 3.303500 48.36000 27.38800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3209624E-04 1.4136146E-02 midg,1,midg; midg,igrid,midg 5.5818573E-02 2.4574064E-02 1,midg,midg; igrid,midg,midg -5.1662996E-03 1.1843762E-02 gauss-seidel spectral radius is 0.9982522 estimated iterations to convergence 190 setup time was (sec) 0.8400000 now iterating at: 08:07:15 rms-change max change #iterations 3.141679 158.7838 at 10iterations 1.317205 56.53642 at 20iterations 0.5580581 21.90477 at 30iterations 0.2365282 8.990425 at 40iterations 9.9938646E-02 4.251835 at 50iterations 4.2550433E-02 1.753586 at 60iterations 1.7939178E-02 0.6817474 at 70iterations 7.6538017E-03 0.2892962 at 80iterations 3.2614609E-03 0.1333055 at 90iterations 1.4091081E-03 6.0735703E-02 at 100iterations 6.2626379E-04 2.7434349E-02 at 110iterations 2.9426283E-04 1.4438629E-02 at 120iterations finished qdiffx linear iterations at : 08:07:23 total time elapsed so far: 9.190000 # loops : 120 mean,max change (kT/e) : 2.9426283E-04 1.4438629E-02 energy calculations done at 9.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.360000 DelPhi exited at 08:07:24 9.367u 0.304s 0:10.07 95.9% 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 08:07:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 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: 2.541969 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): -18.92100 25.52800 ymin,ymax (A): 16.84900 79.87100 zmin,zma (A): 2.529000 52.24700 x,y,z range (A): 44.44900 63.02200 49.71800 scale (grids/A): 2.541969 object centre (A): 3.303500 48.36000 27.38800 number of atom coordinates read : 2382 total number of charged atoms : 2245 net assigned charge : 9.000023 assigned positive charge : 359.1702 centred at (gu) : 90.93153 83.42500 96.87994 assigned negative charge : -350.1709 centred at (gu) : 90.37701 83.86828 96.80231 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 128440 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22167 grid for indexing accessible points = 1.400000 m= 60126 mr = 90268 m= 17898 mr = 47559 m= 3156 mr = 13532 m= 276 mr = 2192 m= 3 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 188 time to turn everything in is 1.220000 number of dielectric boundary points 56201 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 17943 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) : 1.694646 object centre at (A) : 3.303500 48.36000 27.38800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7261727E-04 0.1989500 midg,1,midg; midg,igrid,midg 0.8040577 0.4797285 1,midg,midg; igrid,midg,midg -6.2689334E-02 0.1517422 gauss-seidel spectral radius is 0.9991447 estimated iterations to convergence 270 setup time was (sec) 1.550000 now iterating at: 08:07:26 rms-change max change #iterations 8.046469 301.3992 at 10iterations 4.508180 123.4290 at 20iterations 2.523350 63.95457 at 30iterations 1.404100 41.31394 at 40iterations 0.7787617 20.36452 at 50iterations 0.4315750 10.42229 at 60iterations 0.2389192 6.011253 at 70iterations 0.1319808 2.940641 at 80iterations 7.2819576E-02 1.833925 at 90iterations 4.0212732E-02 0.9180164 at 100iterations 2.2203442E-02 0.4866586 at 110iterations 1.2215203E-02 0.2762260 at 120iterations 6.7553283E-03 0.1451254 at 130iterations 3.7236363E-03 8.3185196E-02 at 140iterations 2.0588257E-03 4.5633256E-02 at 150iterations 1.1444916E-03 2.7728081E-02 at 160iterations 6.4215082E-04 1.4989853E-02 at 170iterations 3.6748024E-04 9.8190308E-03 at 180iterations finished qdiffx linear iterations at : 08:07:39 total time elapsed so far: 15.10000 # loops : 180 mean,max change (kT/e) : 3.6748024E-04 9.8190308E-03 energy calculations done at 15.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.29000 DelPhi exited at 08:07:40 15.287u 0.330s 0:15.91 98.1% 0+0k 0+0io 0pf+0w