Mon Oct 10 19:32:55 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 Mon Oct 10 2011 at 19:32:55 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2645 !!! WARNING: SEP 220 has a net charge of -0.4750 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: 0.6709512 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): -20.05600 31.59700 ymin,ymax (A): -7.008000 46.05100 zmin,zma (A): 34.68200 87.04601 x,y,z range (A): 51.65300 53.05900 52.36401 scale (grids/A): 0.6709512 object centre (A): 5.770500 19.52150 60.86400 number of atom coordinates read : 2645 total number of charged atoms : 2505 net assigned charge : 1.525007 assigned positive charge : 399.3134 centred at (gu) : 90.47263 90.41523 89.41190 assigned negative charge : -397.7893 centred at (gu) : 90.60920 90.35032 89.39568 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8264 nv = 96 ne = 84 npr = 52675 no. pairs analyzed = 52675 no. exposed pairs = 3379 no. arc points = 23605 no. surface atoms = 1123 nbur = 1522 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 544 mr = 4653 m= 5 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2257 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9417 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1103718E-09 8.6026324E-09 midg,1,midg; midg,igrid,midg -1.1071522E-08 2.4613822E-08 1,midg,midg; igrid,midg,midg 3.7476887E-08 -3.4991242E-08 gauss-seidel spectral radius is 0.9884935 estimated iterations to convergence 76 setup time was (sec) 0.5100000 now iterating at: 19:32:56 rms-change max change #iterations 0.1826618 23.52348 at 10iterations 2.0072499E-02 3.169971 at 20iterations 2.2770464E-03 0.3540058 at 30iterations 2.8738973E-04 4.3327093E-02 at 40iterations 6.7303459E-05 9.7070932E-03 at 50iterations finished qdiffx linear iterations at : 19:32:58 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 6.7303459E-05 9.7070932E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 19:32:59 3.360u 0.179s 0:03.99 88.4% 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 19:32:59 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2645 !!! WARNING: SEP 220 has a net charge of -0.4750 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: 2.012854 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): -20.05600 31.59700 ymin,ymax (A): -7.008000 46.05100 zmin,zma (A): 34.68200 87.04601 x,y,z range (A): 51.65300 53.05900 52.36401 scale (grids/A): 2.012854 object centre (A): 5.770500 19.52150 60.86400 number of atom coordinates read : 2645 total number of charged atoms : 2505 net assigned charge : 1.525007 assigned positive charge : 399.3134 centred at (gu) : 91.41711 91.24512 88.23500 assigned negative charge : -397.7893 centred at (gu) : 91.82737 91.05065 88.18664 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 87597 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23605 grid for indexing accessible points = 1.400000 m= 35459 mr = 61283 m= 6890 mr = 27040 m= 571 mr = 4634 m= 12 mr = 262 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1498 time to turn everything in is 0.6200000 number of dielectric boundary points 37310 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 19820 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) : 0.6709512 object centre at (A) : 5.770500 19.52150 60.86400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0001274E-02 -1.5191583E-02 midg,1,midg; midg,igrid,midg -5.5683409E-03 3.8316350E-02 1,midg,midg; igrid,midg,midg 2.1715749E-03 -6.4474246E-03 gauss-seidel spectral radius is 0.9987795 estimated iterations to convergence 227 setup time was (sec) 0.9100000 now iterating at: 19:33:00 rms-change max change #iterations 4.812875 209.3993 at 10iterations 2.342907 89.51705 at 20iterations 1.142177 31.60575 at 30iterations 0.5601369 16.82446 at 40iterations 0.2729590 7.640877 at 50iterations 0.1332318 3.538155 at 60iterations 6.5317266E-02 1.862694 at 70iterations 3.1814899E-02 0.8798971 at 80iterations 1.5557277E-02 0.4501801 at 90iterations 7.6279761E-03 0.2192078 at 100iterations 3.7555238E-03 0.1095673 at 110iterations 1.8675440E-03 5.2864075E-02 at 120iterations finished qdiffx linear iterations at : 19:33:07 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.8675440E-03 5.2864075E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 19:33:08 7.725u 0.225s 0:08.50 93.4% 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 19:33:08 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2645 !!! WARNING: SEP 220 has a net charge of -0.4750 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: 3.019280 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): -20.05600 31.59700 ymin,ymax (A): -7.008000 46.05100 zmin,zma (A): 34.68200 87.04601 x,y,z range (A): 51.65300 53.05900 52.36401 scale (grids/A): 3.019280 object centre (A): 5.770500 19.52150 60.86400 number of atom coordinates read : 2645 total number of charged atoms : 2505 net assigned charge : 1.525007 assigned positive charge : 399.3134 centred at (gu) : 92.12553 91.86753 87.35241 assigned negative charge : -397.7893 centred at (gu) : 92.74106 91.57593 87.28004 start vw surface at 0.1600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 201446 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23605 grid for indexing accessible points = 1.400000 m= 109788 mr = 147565 m= 45635 mr = 91246 m= 12920 mr = 37671 m= 2460 mr = 10098 m= 211 mr = 1775 m= 2 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 5217 time to turn everything in is 1.650000 number of dielectric boundary points 83980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 20040 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) : 2.012854 object centre at (A) : 5.770500 19.52150 60.86400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2320859 2.4057403E-02 midg,1,midg; midg,igrid,midg -0.1670186 0.4251722 1,midg,midg; igrid,midg,midg -0.2056753 0.1878034 gauss-seidel spectral radius is 0.9992958 estimated iterations to convergence 297 setup time was (sec) 1.950000 now iterating at: 19:33:10 rms-change max change #iterations 11.04353 410.7397 at 10iterations 6.542668 127.4479 at 20iterations 3.870145 84.25490 at 30iterations 2.280633 41.08309 at 40iterations 1.342808 23.44881 at 50iterations 0.7878698 13.75619 at 60iterations 0.4624783 8.313479 at 70iterations 0.2705210 4.581484 at 80iterations 0.1579385 2.871964 at 90iterations 9.2601486E-02 1.701390 at 100iterations 5.4123696E-02 0.9419422 at 110iterations 3.1600717E-02 0.5152241 at 120iterations 1.8446855E-02 0.2882881 at 130iterations 1.0765922E-02 0.1822090 at 140iterations 6.2981988E-03 9.6876144E-02 at 150iterations 3.6735197E-03 6.2429428E-02 at 160iterations 2.1476462E-03 3.8299561E-02 at 170iterations 1.2577724E-03 2.0088553E-02 at 180iterations finished qdiffx linear iterations at : 19:33:21 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 1.2577724E-03 2.0088553E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 19:33:21 12.806u 0.256s 0:13.41 97.3% 0+0k 0+0io 0pf+0w