Tue Oct 11 03:36:12 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 Tue Oct 11 2011 at 03:36:12 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2273 !!! WARNING: SEP 331 has a net charge of -0.4750 !!! WARNING: HIR 435 has a net charge of 0.5140 !!! WARNING: ASP 461 has a net charge of -0.2720 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: 0.5547073 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): -27.61800 36.56000 ymin,ymax (A): -7.195000 41.56100 zmin,zma (A): 4.869000 51.40300 x,y,z range (A): 64.17799 48.75600 46.53400 scale (grids/A): 0.5547073 object centre (A): 4.470999 17.18300 28.13600 number of atom coordinates read : 2273 total number of charged atoms : 2186 net assigned charge : -6.232980 assigned positive charge : 339.4052 centred at (gu) : 91.99380 89.98969 89.88744 assigned negative charge : -345.6387 centred at (gu) : 92.03138 90.06256 89.78615 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 4612 nv = 96 ne = 84 npr = 45615 no. pairs analyzed = 45615 no. exposed pairs = 2989 no. arc points = 21409 no. surface atoms = 999 nbur = 1274 mkacc time = 0.1100000 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= 190 mr = 2262 m= 0 mr = 10 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 2530 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2158 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 5984 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2957220E-09 1.7026994E-10 midg,1,midg; midg,igrid,midg -2.1393975E-11 -1.0521599E-09 1,midg,midg; igrid,midg,midg -1.7216280E-10 -1.3011400E-09 gauss-seidel spectral radius is 0.9831871 estimated iterations to convergence 63 setup time was (sec) 0.5700000 now iterating at: 03:36:13 rms-change max change #iterations 7.1787544E-02 13.19006 at 10iterations 4.8469868E-03 0.8403988 at 20iterations 3.2948842E-04 5.9719086E-02 at 30iterations 2.3603336E-05 4.1656494E-03 at 40iterations 1.6269670E-06 2.8657913E-04 at 50iterations finished qdiffx linear iterations at : 03:36:16 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.6269670E-06 2.8657913E-04 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 03:36:17 3.542u 0.178s 0:04.12 90.0% 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 Tue Oct 11 2011 at 03:36:17 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2273 !!! WARNING: SEP 331 has a net charge of -0.4750 !!! WARNING: HIR 435 has a net charge of 0.5140 !!! WARNING: ASP 461 has a net charge of -0.2720 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: 1.664122 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): -27.61800 36.56000 ymin,ymax (A): -7.195000 41.56100 zmin,zma (A): 4.869000 51.40300 x,y,z range (A): 64.17799 48.75600 46.53400 scale (grids/A): 1.664122 object centre (A): 4.470999 17.18300 28.13600 number of atom coordinates read : 2273 total number of charged atoms : 2186 net assigned charge : -6.232980 assigned positive charge : 339.4052 centred at (gu) : 95.98116 89.96864 89.66187 assigned negative charge : -345.6387 centred at (gu) : 96.09396 90.18762 89.35825 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 50617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21409 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 14576 mr = 33028 m= 1520 mr = 9666 m= 33 mr = 707 m= 0 mr = 4 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.4200000 number of dielectric boundary points 23341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 217 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 16854 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) : 0.5547073 object centre at (A) : 4.470999 17.18300 28.13600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2339607E-03 6.8878760E-03 midg,1,midg; midg,igrid,midg 2.4713608E-03 -8.9797368E-03 1,midg,midg; igrid,midg,midg -2.1440145E-03 -2.6049934E-02 gauss-seidel spectral radius is 0.9981787 estimated iterations to convergence 186 setup time was (sec) 0.7000000 now iterating at: 03:36:18 rms-change max change #iterations 2.985055 140.9870 at 10iterations 1.236442 54.17503 at 20iterations 0.5151367 23.33355 at 30iterations 0.2147025 8.111023 at 40iterations 8.8604636E-02 3.672536 at 50iterations 3.6903173E-02 1.644257 at 60iterations 1.5326853E-02 0.6335559 at 70iterations 6.3576493E-03 0.2580633 at 80iterations 2.6456008E-03 0.1065216 at 90iterations 1.1035085E-03 4.4665337E-02 at 100iterations 4.5870460E-04 1.7942429E-02 at 110iterations 1.9104927E-04 7.8582764E-03 at 120iterations finished qdiffx linear iterations at : 03:36:24 total time elapsed so far: 7.140000 # loops : 120 mean,max change (kT/e) : 1.9104927E-04 7.8582764E-03 energy calculations done at 7.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.340000 DelPhi exited at 03:36:25 7.346u 0.199s 0:07.86 95.8% 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 Tue Oct 11 2011 at 03:36:25 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2273 !!! WARNING: SEP 331 has a net charge of -0.4750 !!! WARNING: HIR 435 has a net charge of 0.5140 !!! WARNING: ASP 461 has a net charge of -0.2720 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: 2.496183 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): -27.61800 36.56000 ymin,ymax (A): -7.195000 41.56100 zmin,zma (A): 4.869000 51.40300 x,y,z range (A): 64.17799 48.75600 46.53400 scale (grids/A): 2.496183 object centre (A): 4.470999 17.18300 28.13600 number of atom coordinates read : 2273 total number of charged atoms : 2186 net assigned charge : -6.232980 assigned positive charge : 339.4052 centred at (gu) : 98.97171 89.95274 89.49254 assigned negative charge : -345.6387 centred at (gu) : 99.14077 90.28140 89.03741 start vw surface at 0.1400000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 117777 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21409 grid for indexing accessible points = 1.400000 m= 50671 mr = 81447 m= 14191 mr = 39129 m= 2230 mr = 10331 m= 123 mr = 1462 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 231 time to turn everything in is 0.9100000 number of dielectric boundary points 52582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 17466 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) : 1.664122 object centre at (A) : 4.470999 17.18300 28.13600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6126395E-02 0.1573174 midg,1,midg; midg,igrid,midg 3.2366201E-02 -0.1116478 1,midg,midg; igrid,midg,midg -0.1031263 -0.3460980 gauss-seidel spectral radius is 0.9991177 estimated iterations to convergence 266 setup time was (sec) 1.190000 now iterating at: 03:36:26 rms-change max change #iterations 7.634373 287.8701 at 10iterations 4.206595 112.1599 at 20iterations 2.312076 59.89931 at 30iterations 1.265628 29.05851 at 40iterations 0.6915772 19.60128 at 50iterations 0.3783272 8.470829 at 60iterations 0.2059136 4.667759 at 70iterations 0.1121538 2.399478 at 80iterations 6.0973242E-02 1.415937 at 90iterations 3.3259582E-02 0.7576675 at 100iterations 1.8090341E-02 0.4328003 at 110iterations 9.8367687E-03 0.2245979 at 120iterations 5.3501171E-03 0.1230001 at 130iterations 2.9147114E-03 6.3751221E-02 at 140iterations 1.5846658E-03 4.1803360E-02 at 150iterations 8.6056761E-04 2.1503448E-02 at 160iterations 4.6746689E-04 1.0757446E-02 at 170iterations 2.5496221E-04 5.2976608E-03 at 180iterations finished qdiffx linear iterations at : 03:36:36 total time elapsed so far: 11.15000 # loops : 180 mean,max change (kT/e) : 2.5496221E-04 5.2976608E-03 energy calculations done at 11.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.33000 DelPhi exited at 03:36:36 11.336u 0.193s 0:11.87 97.0% 0+0k 0+0io 0pf+0w