Wed Dec 28 11:04:54 PST 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 Wed Dec 28 2011 at 11:04:54 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.5702478 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): -35.92000 11.60600 ymin,ymax (A): -0.1480000 42.90600 zmin,zma (A): -5.482000 56.94700 x,y,z range (A): 47.52600 43.05400 62.42900 scale (grids/A): 0.5702478 object centre (A): -12.15700 21.37900 25.73250 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 291.4000 centred at (gu) : 90.14105 89.59821 91.18142 assigned negative charge : -289.4003 centred at (gu) : 90.02957 89.75101 91.19608 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4292 nv = 96 ne = 84 npr = 39923 no. pairs analyzed = 39923 no. exposed pairs = 2446 no. arc points = 17491 no. surface atoms = 838 nbur = 1132 mkacc time = 7.9999998E-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 = 1.512000 m= 206 mr = 2323 m= 0 mr = 20 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2155 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1859 ## 272 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 5430 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4580142E-10 1.9813803E-10 midg,1,midg; midg,igrid,midg 2.0381243E-09 -1.1783911E-09 1,midg,midg; igrid,midg,midg -8.3091528E-10 1.4872438E-09 gauss-seidel spectral radius is 0.9840515 estimated iterations to convergence 65 setup time was (sec) 0.5300000 now iterating at: 11:04:55 rms-change max change #iterations 7.4892223E-02 15.19904 at 10iterations 5.4480103E-03 1.051662 at 20iterations 4.0673648E-04 7.5014114E-02 at 30iterations 3.0934261E-05 5.2042007E-03 at 40iterations 2.1964179E-06 4.5776367E-04 at 50iterations finished qdiffx linear iterations at : 11:04:58 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 2.1964179E-06 4.5776367E-04 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.810000 DelPhi exited at 11:04:58 3.818u 0.234s 0:04.60 87.8% 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 Wed Dec 28 2011 at 11:04:59 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.710743 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): -35.92000 11.60600 ymin,ymax (A): -0.1480000 42.90600 zmin,zma (A): -5.482000 56.94700 x,y,z range (A): 47.52600 43.05400 62.42900 scale (grids/A): 1.710743 object centre (A): -12.15700 21.37900 25.73250 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 291.4000 centred at (gu) : 90.42305 88.79459 93.54408 assigned negative charge : -289.4003 centred at (gu) : 90.08899 89.25336 93.58858 start vw surface at 0.1400000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 46520 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17491 grid for indexing accessible points = 1.400000 m= 16454 mr = 31431 m= 2051 mr = 12334 m= 60 mr = 1187 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 20116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 14252 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) : 0.5702478 object centre at (A) : -12.15700 21.37900 25.73250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5280844E-02 2.5441434E-02 midg,1,midg; midg,igrid,midg 1.4385808E-03 -7.8323232E-03 1,midg,midg; igrid,midg,midg -2.9628538E-03 5.6807976E-04 gauss-seidel spectral radius is 0.9982327 estimated iterations to convergence 189 setup time was (sec) 0.7500000 now iterating at: 11:05:00 rms-change max change #iterations 2.901580 163.4628 at 10iterations 1.220446 55.68224 at 20iterations 0.5143470 21.19753 at 30iterations 0.2165801 9.028364 at 40iterations 9.1111787E-02 3.792967 at 50iterations 3.8494743E-02 1.569640 at 60iterations 1.6185030E-02 0.6882849 at 70iterations 6.8406300E-03 0.2861137 at 80iterations 2.8958884E-03 0.1254005 at 90iterations 1.2212617E-03 5.1361084E-02 at 100iterations 5.1328004E-04 2.0626068E-02 at 110iterations 2.1689553E-04 8.6250305E-03 at 120iterations finished qdiffx linear iterations at : 11:05:08 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 2.1689553E-04 8.6250305E-03 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.370000 DelPhi exited at 11:05:09 9.372u 0.259s 0:09.95 96.6% 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 Wed Dec 28 2011 at 11:05:09 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.566115 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): -35.92000 11.60600 ymin,ymax (A): -0.1480000 42.90600 zmin,zma (A): -5.482000 56.94700 x,y,z range (A): 47.52600 43.05400 62.42900 scale (grids/A): 2.566115 object centre (A): -12.15700 21.37900 25.73250 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 291.4000 centred at (gu) : 90.63448 88.19196 95.31610 assigned negative charge : -289.4003 centred at (gu) : 90.13357 88.88010 95.38298 start vw surface at 0.1200000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 107590 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17491 grid for indexing accessible points = 1.400000 m= 53818 mr = 76284 m= 18366 mr = 44126 m= 3427 mr = 14984 m= 290 mr = 2498 m= 9 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8400000 number of dielectric boundary points 45444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 14699 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) : 1.710743 object centre at (A) : -12.15700 21.37900 25.73250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1382623 0.3283690 midg,1,midg; midg,igrid,midg -1.1980328E-02 -9.3226910E-02 1,midg,midg; igrid,midg,midg -5.7581097E-02 -1.8304756E-02 gauss-seidel spectral radius is 0.9991199 estimated iterations to convergence 266 setup time was (sec) 1.150000 now iterating at: 11:05:10 rms-change max change #iterations 7.160155 276.3062 at 10iterations 3.911671 114.2134 at 20iterations 2.139427 52.10126 at 30iterations 1.169037 28.10637 at 40iterations 0.6397192 15.72226 at 50iterations 0.3488400 8.802416 at 60iterations 0.1896798 4.849525 at 70iterations 0.1033089 2.634364 at 80iterations 5.6326259E-02 1.252353 at 90iterations 3.0653926E-02 0.7517977 at 100iterations 1.6689043E-02 0.4056549 at 110iterations 9.1152228E-03 0.2434759 at 120iterations 4.9690497E-03 0.1135750 at 130iterations 2.7003221E-03 6.4825058E-02 at 140iterations 1.4718209E-03 3.6346436E-02 at 150iterations 8.0130552E-04 1.9027710E-02 at 160iterations 4.3712702E-04 1.1042595E-02 at 170iterations 2.3810637E-04 5.5103302E-03 at 180iterations finished qdiffx linear iterations at : 11:05:20 total time elapsed so far: 10.78000 # loops : 180 mean,max change (kT/e) : 2.3810637E-04 5.5103302E-03 energy calculations done at 10.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.96000 DelPhi exited at 11:05:20 10.960u 0.276s 0:11.78 95.3% 0+0k 0+0io 0pf+0w