Sun Oct 9 11:25:41 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 11:25:41 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2771 !!! WARNING: HIR 211 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5860468 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): -20.65600 34.61600 ymin,ymax (A): 19.89200 72.82000 zmin,zma (A): 31.15700 91.90300 x,y,z range (A): 55.27200 52.92800 60.74600 scale (grids/A): 0.5860468 object centre (A): 6.980000 46.35600 61.53000 number of atom coordinates read : 2771 total number of charged atoms : 2627 net assigned charge : -3.985983 assigned positive charge : 403.0973 centred at (gu) : 90.70063 88.11075 90.41843 assigned negative charge : -407.0848 centred at (gu) : 90.82468 88.13850 90.47425 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6557 nv = 96 ne = 84 npr = 54816 no. pairs analyzed = 54816 no. exposed pairs = 3728 no. arc points = 26905 no. surface atoms = 1256 nbur = 1515 mkacc time = 8.9999996E-02 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 = 1.456000 m= 301 mr = 3267 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.2100000 number of dielectric boundary points 3578 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2616 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8072 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7380384E-10 -2.6712808E-09 midg,1,midg; midg,igrid,midg -5.4791022E-10 -1.1285121E-09 1,midg,midg; igrid,midg,midg 1.6395750E-09 -4.8665147E-09 gauss-seidel spectral radius is 0.9849688 estimated iterations to convergence 67 setup time was (sec) 0.4100000 now iterating at: 11:25:41 rms-change max change #iterations 9.9547707E-02 18.46232 at 10iterations 7.9940017E-03 1.134434 at 20iterations 6.3488772E-04 9.8773956E-02 at 30iterations 5.5682911E-05 8.4502697E-03 at 40iterations 6.6996777E-06 1.2612343E-03 at 50iterations finished qdiffx linear iterations at : 11:25:44 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 6.6996777E-06 1.2612343E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 11:25:45 3.536u 0.180s 0:04.13 89.8% 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 11:25:45 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2771 !!! WARNING: HIR 211 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.758140 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): -20.65600 34.61600 ymin,ymax (A): 19.89200 72.82000 zmin,zma (A): 31.15700 91.90300 x,y,z range (A): 55.27200 52.92800 60.74600 scale (grids/A): 1.758140 object centre (A): 6.980000 46.35600 61.53000 number of atom coordinates read : 2771 total number of charged atoms : 2627 net assigned charge : -3.985983 assigned positive charge : 403.0973 centred at (gu) : 92.10107 84.33141 91.25411 assigned negative charge : -407.0848 centred at (gu) : 92.47404 84.41544 91.42244 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 71587 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26905 grid for indexing accessible points = 1.400000 m= 23640 mr = 47332 m= 3171 mr = 16208 m= 127 mr = 1713 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 242 time to turn everything in is 0.3500000 number of dielectric boundary points 33261 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 189 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 20487 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) : 0.5860468 object centre at (A) : 6.980000 46.35600 61.53000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3605910E-02 6.5536774E-03 midg,1,midg; midg,igrid,midg 7.2155474E-03 -7.8441110E-03 1,midg,midg; igrid,midg,midg -1.3371324E-02 -3.1285681E-02 gauss-seidel spectral radius is 0.9984426 estimated iterations to convergence 201 setup time was (sec) 0.5900000 now iterating at: 11:25:46 rms-change max change #iterations 3.710714 152.5240 at 10iterations 1.636772 64.59573 at 20iterations 0.7277163 29.88989 at 30iterations 0.3227057 11.22017 at 40iterations 0.1430027 5.085896 at 50iterations 6.3495092E-02 2.171062 at 60iterations 2.8235340E-02 0.9754925 at 70iterations 1.2547534E-02 0.6132698 at 80iterations 5.5554113E-03 0.1934931 at 90iterations 2.4901615E-03 8.3648682E-02 at 100iterations 1.1068300E-03 3.9248466E-02 at 110iterations 4.9448904E-04 1.6654968E-02 at 120iterations finished qdiffx linear iterations at : 11:25:53 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 4.9448904E-04 1.6654968E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.190000 DelPhi exited at 11:25:54 8.189u 0.207s 0:08.73 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 Sun Oct 9 2011 at 11:25:54 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2771 !!! WARNING: HIR 211 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.637211 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): -20.65600 34.61600 ymin,ymax (A): 19.89200 72.82000 zmin,zma (A): 31.15700 91.90300 x,y,z range (A): 55.27200 52.92800 60.74600 scale (grids/A): 2.637211 object centre (A): 6.980000 46.35600 61.53000 number of atom coordinates read : 2771 total number of charged atoms : 2627 net assigned charge : -3.985983 assigned positive charge : 403.0973 centred at (gu) : 93.15154 81.49678 91.88093 assigned negative charge : -407.0848 centred at (gu) : 93.71096 81.62307 92.13374 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 166021 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26905 grid for indexing accessible points = 1.400000 m= 77877 mr = 116057 m= 25652 mr = 61025 m= 5295 mr = 19398 m= 567 mr = 3609 m= 23 mr = 293 m= 0 mr = 4 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 863 time to turn everything in is 0.8900000 number of dielectric boundary points 75049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 21007 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) : 1.758140 object centre at (A) : 6.980000 46.35600 61.53000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2095955 0.3920312 midg,1,midg; midg,igrid,midg 0.1354589 -0.1664492 1,midg,midg; igrid,midg,midg -0.2069009 -0.3544271 gauss-seidel spectral radius is 0.9992172 estimated iterations to convergence 282 setup time was (sec) 1.140000 now iterating at: 11:25:55 rms-change max change #iterations 9.299463 305.1629 at 10iterations 5.433780 139.8644 at 20iterations 3.132585 71.27132 at 30iterations 1.804011 39.92156 at 40iterations 1.030272 22.62723 at 50iterations 0.5891677 11.25218 at 60iterations 0.3355699 6.572547 at 70iterations 0.1908756 3.521394 at 80iterations 0.1083608 2.027157 at 90iterations 6.1423130E-02 1.249071 at 100iterations 3.4874462E-02 0.6693497 at 110iterations 1.9744096E-02 0.3838406 at 120iterations 1.1179021E-02 0.2121906 at 130iterations 6.3356441E-03 0.1256084 at 140iterations 3.5830860E-03 6.8851471E-02 at 150iterations 2.0284120E-03 3.7723541E-02 at 160iterations 1.1458321E-03 2.0929337E-02 at 170iterations 6.4723782E-04 1.2150764E-02 at 180iterations finished qdiffx linear iterations at : 11:26:07 total time elapsed so far: 13.05000 # loops : 180 mean,max change (kT/e) : 6.4723782E-04 1.2150764E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 11:26:07 13.176u 0.217s 0:13.67 97.8% 0+0k 0+0io 0pf+0w