Wed Dec 28 11:01:34 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+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 Wed Dec 28 2011 at 11:01:34 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6437497 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): -5.357000 34.68300 ymin,ymax (A): -3.396000 49.37400 zmin,zma (A): -24.42700 30.87400 x,y,z range (A): 40.04000 52.77000 55.30100 scale (grids/A): 0.6437497 object centre (A): 14.66300 22.98900 3.223500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 90.72350 92.33167 90.24895 assigned negative charge : -285.8263 centred at (gu) : 90.83955 92.49021 90.18779 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5610 nv = 96 ne = 84 npr = 40249 no. pairs analyzed = 40249 no. exposed pairs = 2460 no. arc points = 17319 no. surface atoms = 832 nbur = 1132 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 289 mr = 3144 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2500000 number of dielectric boundary points 2715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1688 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6484 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9833322E-09 9.9556416E-09 midg,1,midg; midg,igrid,midg 1.1236065E-08 -1.9410972E-08 1,midg,midg; igrid,midg,midg 1.2443968E-08 -8.6792404E-09 gauss-seidel spectral radius is 0.9874406 estimated iterations to convergence 73 setup time was (sec) 0.5200000 now iterating at: 11:01:58 rms-change max change #iterations 0.1252290 18.86355 at 10iterations 1.2528424E-02 2.080830 at 20iterations 1.2426294E-03 0.2109489 at 30iterations 1.2476386E-04 1.8737793E-02 at 40iterations 1.2436433E-05 2.0484924E-03 at 50iterations finished qdiffx linear iterations at : 11:02:02 total time elapsed so far: 4.620000 # loops : 50 mean,max change (kT/e) : 1.2436433E-05 2.0484924E-03 energy calculations done at 4.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.790000 DelPhi exited at 11:02:05 4.794u 0.447s 0:30.26 17.2% 0+0k 0+0io 6pf+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 11:02:05 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.931249 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): -5.357000 34.68300 ymin,ymax (A): -3.396000 49.37400 zmin,zma (A): -24.42700 30.87400 x,y,z range (A): 40.04000 52.77000 55.30100 scale (grids/A): 1.931249 object centre (A): 14.66300 22.98900 3.223500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 92.17063 96.99528 90.74681 assigned negative charge : -285.8263 centred at (gu) : 92.51875 97.47081 90.56346 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 59825 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17319 grid for indexing accessible points = 1.400000 m= 22539 mr = 41431 m= 3620 mr = 17229 m= 204 mr = 2485 m= 3 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1410 time to turn everything in is 0.5000000 number of dielectric boundary points 24964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 14464 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) : 0.6437497 object centre at (A) : 14.66300 22.98900 3.223500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1271295E-02 8.5241636E-03 midg,1,midg; midg,igrid,midg 3.3680193E-02 -1.7965494E-02 1,midg,midg; igrid,midg,midg 7.2905575E-03 -5.2513992E-03 gauss-seidel spectral radius is 0.9985940 estimated iterations to convergence 211 setup time was (sec) 0.8400000 now iterating at: 11:02:06 rms-change max change #iterations 3.643021 159.6255 at 10iterations 1.687789 60.85729 at 20iterations 0.7834277 26.51008 at 30iterations 0.3624920 15.00755 at 40iterations 0.1677060 5.998205 at 50iterations 7.7253498E-02 2.612846 at 60iterations 3.5904586E-02 1.320220 at 70iterations 1.6583951E-02 0.6488600 at 80iterations 7.6988796E-03 0.2652740 at 90iterations 3.5598474E-03 0.1367264 at 100iterations 1.6532632E-03 5.6823134E-02 at 110iterations 7.6618092E-04 2.6897430E-02 at 120iterations finished qdiffx linear iterations at : 11:02:17 total time elapsed so far: 11.48000 # loops : 120 mean,max change (kT/e) : 7.6618092E-04 2.6897430E-02 energy calculations done at 11.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.65000 DelPhi exited at 11:02:19 11.657u 0.513s 0:14.66 82.9% 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 Wed Dec 28 2011 at 11:02:20 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.896873 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): -5.357000 34.68300 ymin,ymax (A): -3.396000 49.37400 zmin,zma (A): -24.42700 30.87400 x,y,z range (A): 40.04000 52.77000 55.30100 scale (grids/A): 2.896873 object centre (A): 14.66300 22.98900 3.223500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 93.25584 100.4930 91.12036 assigned negative charge : -285.8263 centred at (gu) : 93.77819 101.2062 90.84518 start vw surface at 0.1000000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 138110 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17319 grid for indexing accessible points = 1.400000 m= 71688 mr = 99861 m= 27129 mr = 59703 m= 6640 mr = 22753 m= 936 mr = 5325 m= 54 mr = 649 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 4571 time to turn everything in is 1.440000 number of dielectric boundary points 56236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 14656 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) : 1.931249 object centre at (A) : 14.66300 22.98900 3.223500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9910481 -1.7322246E-03 midg,1,midg; midg,igrid,midg 0.3317105 -0.1925136 1,midg,midg; igrid,midg,midg 3.5260014E-02 -3.4630280E-02 gauss-seidel spectral radius is 0.9992344 estimated iterations to convergence 285 setup time was (sec) 1.920000 now iterating at: 11:02:23 rms-change max change #iterations 8.566403 375.8544 at 10iterations 4.924580 114.0028 at 20iterations 2.802095 61.51316 at 30iterations 1.594097 32.35535 at 40iterations 0.9074455 18.31861 at 50iterations 0.5159636 10.64863 at 60iterations 0.2938069 5.827689 at 70iterations 0.1664709 3.650917 at 80iterations 9.4421349E-02 1.950182 at 90iterations 5.3447757E-02 1.128352 at 100iterations 3.0422352E-02 0.5986443 at 110iterations 1.7291674E-02 0.3367405 at 120iterations 9.7870333E-03 0.1983109 at 130iterations 5.5699698E-03 0.1079445 at 140iterations 3.1592413E-03 6.0894012E-02 at 150iterations 1.7958694E-03 3.4329414E-02 at 160iterations 1.0210562E-03 2.1150589E-02 at 170iterations 5.8044755E-04 1.1305809E-02 at 180iterations finished qdiffx linear iterations at : 11:02:42 total time elapsed so far: 21.04000 # loops : 180 mean,max change (kT/e) : 5.8044755E-04 1.1305809E-02 energy calculations done at 21.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.22000 DelPhi exited at 11:02:43 21.225u 0.723s 0:22.65 96.8% 0+0k 0+0io 0pf+0w