Tue Oct 11 08:33:09 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 08:33:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2108 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: 0.7187853 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): -8.488000 38.40700 ymin,ymax (A): -30.12200 19.40600 zmin,zma (A): 3.758000 46.38800 x,y,z range (A): 46.89500 49.52800 42.63000 scale (grids/A): 0.7187853 object centre (A): 14.95950 -5.358000 25.07300 number of atom coordinates read : 2108 total number of charged atoms : 1980 net assigned charge : 6.500009 assigned positive charge : 321.1839 centred at (gu) : 90.60728 89.22205 90.27943 assigned negative charge : -314.6841 centred at (gu) : 90.48418 89.26777 90.38206 start vw surface at 0.1300000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7467 nv = 96 ne = 84 npr = 42175 no. pairs analyzed = 42175 no. exposed pairs = 2493 no. arc points = 17149 no. surface atoms = 855 nbur = 1253 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 518 mr = 4417 m= 0 mr = 88 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1523 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8110 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2881112E-07 4.5768607E-09 midg,1,midg; midg,igrid,midg 1.1585107E-07 3.6200799E-08 1,midg,midg; igrid,midg,midg -7.3632633E-09 1.6703331E-07 gauss-seidel spectral radius is 0.9899105 estimated iterations to convergence 81 setup time was (sec) 0.6200000 now iterating at: 08:33:10 rms-change max change #iterations 0.2120529 39.53258 at 10iterations 2.7917404E-02 3.537366 at 20iterations 3.6495700E-03 0.5095308 at 30iterations 5.6066754E-04 7.7049255E-02 at 40iterations 1.2994996E-04 1.6576409E-02 at 50iterations finished qdiffx linear iterations at : 08:33:14 total time elapsed so far: 4.420000 # loops : 50 mean,max change (kT/e) : 1.2994996E-04 1.6576409E-02 energy calculations done at 4.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 08:33:14 4.632u 0.417s 0:05.36 94.0% 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 Tue Oct 11 2011 at 08:33:14 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 = 2108 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: 2.156356 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): -8.488000 38.40700 ymin,ymax (A): -30.12200 19.40600 zmin,zma (A): 3.758000 46.38800 x,y,z range (A): 46.89500 49.52800 42.63000 scale (grids/A): 2.156356 object centre (A): 14.95950 -5.358000 25.07300 number of atom coordinates read : 2108 total number of charged atoms : 1980 net assigned charge : 6.500009 assigned positive charge : 321.1839 centred at (gu) : 91.82192 87.66619 90.83801 assigned negative charge : -314.6841 centred at (gu) : 91.45286 87.80337 91.14644 start vw surface at 0.1200000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 79227 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17149 grid for indexing accessible points = 1.400000 m= 32902 mr = 57065 m= 6566 mr = 25423 m= 580 mr = 4431 m= 18 mr = 293 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 32081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 15743 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) : 0.7187853 object centre at (A) : 14.95950 -5.358000 25.07300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6342226E-02 2.4529936E-02 midg,1,midg; midg,igrid,midg 4.3297768E-02 3.7933253E-02 1,midg,midg; igrid,midg,midg -4.2655036E-02 3.5398066E-02 gauss-seidel spectral radius is 0.9988652 estimated iterations to convergence 235 setup time was (sec) 1.160000 now iterating at: 08:33:16 rms-change max change #iterations 4.766469 196.3739 at 10iterations 2.373137 86.12823 at 20iterations 1.194722 37.95359 at 30iterations 0.5986953 17.78612 at 40iterations 0.3005759 8.819723 at 50iterations 0.1505217 4.305502 at 60iterations 7.5684696E-02 2.080498 at 70iterations 3.8074519E-02 1.051485 at 80iterations 1.9188207E-02 0.5839767 at 90iterations 9.7290268E-03 0.3228283 at 100iterations 4.9490556E-03 0.1620770 at 110iterations 2.5591070E-03 7.5569153E-02 at 120iterations finished qdiffx linear iterations at : 08:33:26 total time elapsed so far: 10.93000 # loops : 120 mean,max change (kT/e) : 2.5591070E-03 7.5569153E-02 energy calculations done at 10.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.15000 DelPhi exited at 08:33:26 11.153u 0.483s 0:11.92 97.5% 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 08:33:26 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 = 2108 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: 3.234534 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): -8.488000 38.40700 ymin,ymax (A): -30.12200 19.40600 zmin,zma (A): 3.758000 46.38800 x,y,z range (A): 46.89500 49.52800 42.63000 scale (grids/A): 3.234534 object centre (A): 14.95950 -5.358000 25.07300 number of atom coordinates read : 2108 total number of charged atoms : 1980 net assigned charge : 6.500009 assigned positive charge : 321.1839 centred at (gu) : 92.73283 86.49934 91.25702 assigned negative charge : -314.6841 centred at (gu) : 92.17923 86.70505 91.71965 start vw surface at 0.1500000 fill in re-entrant regions at 1.050000 boundary points on vw surface= 182552 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17149 grid for indexing accessible points = 1.400000 m= 101734 mr = 137063 m= 42782 mr = 85539 m= 12426 mr = 35586 m= 2416 mr = 9800 m= 304 mr = 1720 m= 9 mr = 176 m= 0 mr = 0 time to grow re-entrant surface = 1.420000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.620000 number of dielectric boundary points 72339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.770000 number of grid points assigned charge 15840 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) : 2.156356 object centre at (A) : 14.95950 -5.358000 25.07300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1302114 0.1949798 midg,1,midg; midg,igrid,midg 0.2945386 0.2455320 1,midg,midg; igrid,midg,midg -0.4675500 0.2961598 gauss-seidel spectral radius is 0.9993051 estimated iterations to convergence 299 setup time was (sec) 2.970000 now iterating at: 08:33:30 rms-change max change #iterations 10.57674 455.5798 at 10iterations 6.268352 151.8595 at 20iterations 3.723961 78.68193 at 30iterations 2.209406 46.72066 at 40iterations 1.305892 25.59337 at 50iterations 0.7693656 13.40833 at 60iterations 0.4542184 7.441252 at 70iterations 0.2676999 4.889488 at 80iterations 0.1575660 2.943413 at 90iterations 9.2771836E-02 1.572556 at 100iterations 5.4628272E-02 0.9490280 at 110iterations 3.2354839E-02 0.5113659 at 120iterations 1.9253353E-02 0.3619576 at 130iterations 1.1587341E-02 0.2241898 at 140iterations 7.1426150E-03 0.1344218 at 150iterations 4.5428202E-03 8.4774971E-02 at 160iterations 3.0381025E-03 5.6026459E-02 at 170iterations 2.1630928E-03 3.9421082E-02 at 180iterations finished qdiffx linear iterations at : 08:33:46 total time elapsed so far: 19.84000 # loops : 180 mean,max change (kT/e) : 2.1630928E-03 3.9421082E-02 energy calculations done at 19.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.07000 DelPhi exited at 08:33:47 20.077u 0.480s 0:20.86 98.5% 0+0k 0+0io 0pf+0w