Tue Oct 11 06:18:25 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 06:18:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2072 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7024606 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): -20.77800 29.90100 ymin,ymax (A): -11.89700 30.61000 zmin,zma (A): -8.871000 38.28400 x,y,z range (A): 50.67900 42.50700 47.15500 scale (grids/A): 0.7024606 object centre (A): 4.561501 9.356501 14.70650 number of atom coordinates read : 2072 total number of charged atoms : 1944 net assigned charge : 6.500009 assigned positive charge : 314.9560 centred at (gu) : 91.13302 89.84871 90.98017 assigned negative charge : -308.4562 centred at (gu) : 91.07320 89.78075 90.87331 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7008 nv = 96 ne = 84 npr = 41303 no. pairs analyzed = 41303 no. exposed pairs = 2585 no. arc points = 17429 no. surface atoms = 883 nbur = 1189 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 4021 m= 1 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1681 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7773 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0646660E-09 1.1391059E-07 midg,1,midg; midg,igrid,midg 1.8469352E-08 7.5089808E-08 1,midg,midg; igrid,midg,midg 1.7751432E-08 9.2010261E-08 gauss-seidel spectral radius is 0.9894372 estimated iterations to convergence 79 setup time was (sec) 0.5700000 now iterating at: 06:18:25 rms-change max change #iterations 0.1928056 25.84977 at 10iterations 2.3010811E-02 3.119717 at 20iterations 3.0573322E-03 0.4007225 at 30iterations 4.9409311E-04 7.2901726E-02 at 40iterations 1.2326729E-04 1.3572693E-02 at 50iterations finished qdiffx linear iterations at : 06:18:29 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 1.2326729E-04 1.3572693E-02 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 06:18:29 4.097u 0.261s 0:04.81 90.4% 0+0k 0+0io 5pf+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 06:18:30 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 = 2072 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.107382 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): -20.77800 29.90100 ymin,ymax (A): -11.89700 30.61000 zmin,zma (A): -8.871000 38.28400 x,y,z range (A): 50.67900 42.50700 47.15500 scale (grids/A): 2.107382 object centre (A): 4.561501 9.356501 14.70650 number of atom coordinates read : 2072 total number of charged atoms : 1944 net assigned charge : 6.500009 assigned positive charge : 314.9560 centred at (gu) : 93.39901 89.54607 92.94079 assigned negative charge : -308.4562 centred at (gu) : 93.21976 89.34240 92.62003 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 74218 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17429 grid for indexing accessible points = 1.400000 m= 30253 mr = 52884 m= 5623 mr = 22952 m= 443 mr = 3641 m= 11 mr = 194 m= 0 mr = 3 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 30874 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 94 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 15408 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) : 0.7024606 object centre at (A) : 4.561501 9.356501 14.70650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6026832E-02 2.7529186E-02 midg,1,midg; midg,igrid,midg 1.8660037E-02 2.5293479E-02 1,midg,midg; igrid,midg,midg 4.9229980E-02 3.7785757E-02 gauss-seidel spectral radius is 0.9988166 estimated iterations to convergence 230 setup time was (sec) 0.9900000 now iterating at: 06:18:31 rms-change max change #iterations 4.521581 216.8314 at 10iterations 2.226728 76.72232 at 20iterations 1.100291 36.17830 at 30iterations 0.5424130 17.67981 at 40iterations 0.2684491 8.943086 at 50iterations 0.1326751 4.028275 at 60iterations 6.5590613E-02 1.848027 at 70iterations 3.2461591E-02 1.006500 at 80iterations 1.6171603E-02 0.4873791 at 90iterations 8.0819521E-03 0.2461271 at 100iterations 4.0698401E-03 0.1285725 at 110iterations 2.0999534E-03 6.3789368E-02 at 120iterations finished qdiffx linear iterations at : 06:18:39 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 2.0999534E-03 6.3789368E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.620000 DelPhi exited at 06:18:40 9.620u 0.314s 0:10.42 95.2% 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 06:18:40 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 = 2072 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.161072 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): -20.77800 29.90100 ymin,ymax (A): -11.89700 30.61000 zmin,zma (A): -8.871000 38.28400 x,y,z range (A): 50.67900 42.50700 47.15500 scale (grids/A): 3.161072 object centre (A): 4.561501 9.356501 14.70650 number of atom coordinates read : 2072 total number of charged atoms : 1944 net assigned charge : 6.500009 assigned positive charge : 314.9560 centred at (gu) : 95.09875 89.31908 94.41115 assigned negative charge : -308.4562 centred at (gu) : 94.82965 89.01368 93.93011 start vw surface at 0.1500000 fill in re-entrant regions at 0.9800000 boundary points on vw surface= 171000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17429 grid for indexing accessible points = 1.400000 m= 93953 mr = 127072 m= 38108 mr = 78300 m= 10529 mr = 31283 m= 1884 mr = 8004 m= 190 mr = 1264 m= 11 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.220000 number of dielectric boundary points 69637 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.390000 number of grid points assigned charge 15552 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) : 2.107382 object centre at (A) : 4.561501 9.356501 14.70650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4205859 0.2600449 midg,1,midg; midg,igrid,midg 0.1577050 0.1630303 1,midg,midg; igrid,midg,midg 0.4106004 0.1709976 gauss-seidel spectral radius is 0.9992951 estimated iterations to convergence 297 setup time was (sec) 2.570000 now iterating at: 06:18:43 rms-change max change #iterations 10.18939 456.5862 at 10iterations 6.035724 139.1214 at 20iterations 3.572974 67.44482 at 30iterations 2.109447 44.23464 at 40iterations 1.241609 24.87837 at 50iterations 0.7327884 13.50628 at 60iterations 0.4297361 8.487926 at 70iterations 0.2525839 5.113077 at 80iterations 0.1476534 2.754986 at 90iterations 8.6810455E-02 1.559174 at 100iterations 5.0841685E-02 0.9633734 at 110iterations 2.9967086E-02 0.5460644 at 120iterations 1.7740238E-02 0.3320007 at 130iterations 1.0658129E-02 0.1873217 at 140iterations 6.5319622E-03 0.1150365 at 150iterations 4.1392124E-03 7.7499390E-02 at 160iterations 2.7742223E-03 5.5532455E-02 at 170iterations 1.9666920E-03 3.4151077E-02 at 180iterations finished qdiffx linear iterations at : 06:18:57 total time elapsed so far: 16.45000 # loops : 180 mean,max change (kT/e) : 1.9666920E-03 3.4151077E-02 energy calculations done at 16.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.63000 DelPhi exited at 06:18:58 16.634u 0.305s 0:17.54 96.5% 0+0k 0+0io 0pf+0w