Mon Oct 10 14:14:36 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 14:14:36 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3189 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5761077 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): -9.073000 43.20600 ymin,ymax (A): -28.77300 25.55500 zmin,zma (A): 14.08200 75.87600 x,y,z range (A): 52.27900 54.32800 61.79400 scale (grids/A): 0.5761077 object centre (A): 17.06650 -1.608999 44.97900 number of atom coordinates read : 3189 total number of charged atoms : 3040 net assigned charge : -5.773974 assigned positive charge : 476.6655 centred at (gu) : 89.79361 91.97701 91.31530 assigned negative charge : -482.4407 centred at (gu) : 89.59997 91.87050 91.27066 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6805 nv = 96 ne = 84 npr = 65779 no. pairs analyzed = 65779 no. exposed pairs = 3868 no. arc points = 27133 no. surface atoms = 1295 nbur = 1894 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 = 1.484000 m= 307 mr = 3695 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.4000000 number of dielectric boundary points 3395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2763 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8870 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5316504E-09 -2.7318214E-10 midg,1,midg; midg,igrid,midg -2.1381676E-09 1.7397206E-09 1,midg,midg; igrid,midg,midg -5.5410463E-09 2.6667391E-09 gauss-seidel spectral radius is 0.9844621 estimated iterations to convergence 66 setup time was (sec) 0.6600000 now iterating at: 14:14:37 rms-change max change #iterations 9.9770300E-02 14.12151 at 10iterations 8.0404747E-03 1.183876 at 20iterations 1.2197045E-03 0.2433147 at 30iterations 4.8499292E-04 0.1056747 at 40iterations 2.1441752E-04 4.7153473E-02 at 50iterations finished qdiffx linear iterations at : 14:14:40 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 2.1441752E-04 4.7153473E-02 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 14:14:41 4.149u 0.284s 0:05.17 85.4% 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 Mon Oct 10 2011 at 14:14:41 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3189 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.728323 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): -9.073000 43.20600 ymin,ymax (A): -28.77300 25.55500 zmin,zma (A): 14.08200 75.87600 x,y,z range (A): 52.27900 54.32800 61.79400 scale (grids/A): 1.728323 object centre (A): 17.06650 -1.608999 44.97900 number of atom coordinates read : 3189 total number of charged atoms : 3040 net assigned charge : -5.773974 assigned positive charge : 476.6655 centred at (gu) : 89.37966 95.92990 93.94484 assigned negative charge : -482.4407 centred at (gu) : 88.79938 95.61092 93.81160 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 75147 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27133 grid for indexing accessible points = 1.400000 m= 24068 mr = 52014 m= 2929 mr = 17225 m= 122 mr = 1684 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1200 time to turn everything in is 0.6700000 number of dielectric boundary points 31320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 299 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 23563 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) : 0.5761077 object centre at (A) : 17.06650 -1.608999 44.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9145703E-02 8.4981667E-03 midg,1,midg; midg,igrid,midg -1.9973895E-02 -4.7418857E-03 1,midg,midg; igrid,midg,midg -2.6229085E-02 5.7572708E-04 gauss-seidel spectral radius is 0.9984019 estimated iterations to convergence 198 setup time was (sec) 0.9700000 now iterating at: 14:14:43 rms-change max change #iterations 3.924041 149.4327 at 10iterations 1.721791 57.98030 at 20iterations 0.7570767 25.62032 at 30iterations 0.3341434 10.84975 at 40iterations 0.1473708 5.683989 at 50iterations 6.4885914E-02 2.452694 at 60iterations 2.8789124E-02 0.9197369 at 70iterations 1.2893057E-02 0.4331589 at 80iterations 6.0039731E-03 0.2289267 at 90iterations 3.0218416E-03 0.1194878 at 100iterations 1.7230122E-03 7.2219849E-02 at 110iterations 1.1308704E-03 5.0140381E-02 at 120iterations finished qdiffx linear iterations at : 14:14:51 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 1.1308704E-03 5.0140381E-02 energy calculations done at 9.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.510000 DelPhi exited at 14:14:52 9.517u 0.314s 0:10.22 96.0% 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 14:14:52 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3189 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.592485 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): -9.073000 43.20600 ymin,ymax (A): -28.77300 25.55500 zmin,zma (A): 14.08200 75.87600 x,y,z range (A): 52.27900 54.32800 61.79400 scale (grids/A): 2.592485 object centre (A): 17.06650 -1.608999 44.97900 number of atom coordinates read : 3189 total number of charged atoms : 3040 net assigned charge : -5.773974 assigned positive charge : 476.6655 centred at (gu) : 89.06914 98.89468 95.91692 assigned negative charge : -482.4407 centred at (gu) : 88.19907 98.41631 95.71732 start vw surface at 0.1700000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 174206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27133 grid for indexing accessible points = 1.400000 m= 81798 mr = 126744 m= 25421 mr = 65978 m= 4911 mr = 19840 m= 439 mr = 3471 m= 16 mr = 245 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 3936 time to turn everything in is 1.640000 number of dielectric boundary points 70513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 24297 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) : 1.728323 object centre at (A) : 17.06650 -1.608999 44.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2309648 4.2416945E-02 midg,1,midg; midg,igrid,midg -0.2984070 -4.5162309E-02 1,midg,midg; igrid,midg,midg -0.2066122 -5.1653452E-02 gauss-seidel spectral radius is 0.9992048 estimated iterations to convergence 280 setup time was (sec) 1.970000 now iterating at: 14:14:54 rms-change max change #iterations 9.764512 332.4280 at 10iterations 5.624390 152.8900 at 20iterations 3.224583 75.84411 at 30iterations 1.839776 40.25899 at 40iterations 1.044594 21.95766 at 50iterations 0.5934079 13.13530 at 60iterations 0.3367420 6.811601 at 70iterations 0.1906330 4.567609 at 80iterations 0.1078956 2.106967 at 90iterations 6.1026383E-02 1.167458 at 100iterations 3.4462783E-02 0.6673632 at 110iterations 1.9498182E-02 0.4008832 at 120iterations 1.1057667E-02 0.2135332 at 130iterations 6.3209147E-03 0.1474323 at 140iterations 3.6817542E-03 7.7587128E-02 at 150iterations 2.2068794E-03 4.6852112E-02 at 160iterations 1.4008579E-03 3.6355972E-02 at 170iterations 9.6075825E-04 2.3555756E-02 at 180iterations finished qdiffx linear iterations at : 14:15:08 total time elapsed so far: 15.78000 # loops : 180 mean,max change (kT/e) : 9.6075825E-04 2.3555756E-02 energy calculations done at 15.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.96000 DelPhi exited at 14:15:09 15.963u 0.315s 0:16.98 95.8% 0+0k 0+0io 0pf+0w