Tue Oct 11 03:23:47 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 Tue Oct 11 2011 at 03:23:47 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1121 !!! WARNING: HIT 60 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7462530 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): -6.311000 30.22800 ymin,ymax (A): 1.137000 39.96700 zmin,zma (A): -0.9830000 46.72200 x,y,z range (A): 36.53900 38.83000 47.70500 scale (grids/A): 0.7462530 object centre (A): 11.95850 20.55200 22.86950 number of atom coordinates read : 1121 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.1651 centred at (gu) : 89.35909 89.28669 88.27127 assigned negative charge : -172.6512 centred at (gu) : 89.06474 89.28893 88.29282 start vw surface at 5.0000001E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 4366 nv = 96 ne = 84 npr = 20926 no. pairs analyzed = 20926 no. exposed pairs = 1482 no. arc points = 10838 no. surface atoms = 497 nbur = 624 mkacc time = 3.0000005E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 300 mr = 2249 m= 4 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 3.0000009E-02 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.1000000 number of dielectric boundary points 2365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 933 ## 72 charges are in solution ## iepsmp to db, and charging done at 0.1700000 number of grid points assigned charge 4523 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7180700E-07 7.2913238E-08 midg,1,midg; midg,igrid,midg 1.2902643E-07 9.7538113E-08 1,midg,midg; igrid,midg,midg -8.6274369E-08 2.5705620E-07 gauss-seidel spectral radius is 0.9905407 estimated iterations to convergence 84 setup time was (sec) 0.3000000 now iterating at: 03:23:47 rms-change max change #iterations 0.1865140 31.64390 at 10iterations 2.4922607E-02 4.083495 at 20iterations 3.3492094E-03 0.6001403 at 30iterations 4.5869677E-04 8.7870598E-02 at 40iterations 6.0959588E-05 1.0467529E-02 at 50iterations finished qdiffx linear iterations at : 03:23:50 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 6.0959588E-05 1.0467529E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 03:23:51 3.283u 0.173s 0:03.75 92.0% 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 03:23:51 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1121 !!! WARNING: HIT 60 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.238759 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): -6.311000 30.22800 ymin,ymax (A): 1.137000 39.96700 zmin,zma (A): -0.9830000 46.72200 x,y,z range (A): 36.53900 38.83000 47.70500 scale (grids/A): 2.238759 object centre (A): 11.95850 20.55200 22.86950 number of atom coordinates read : 1121 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.1651 centred at (gu) : 88.07739 87.86006 84.81377 assigned negative charge : -172.6512 centred at (gu) : 87.19458 87.86680 84.87857 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 44937 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10838 grid for indexing accessible points = 1.400000 m= 17324 mr = 29083 m= 3415 mr = 12944 m= 341 mr = 2339 m= 20 mr = 203 m= 0 mr = 10 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 349 time to turn everything in is 0.2300000 number of dielectric boundary points 21458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8456 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) : 0.7462530 object centre at (A) : 11.95850 20.55200 22.86950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8142881E-02 8.9635588E-03 midg,1,midg; midg,igrid,midg 4.2274091E-02 2.8517239E-02 1,midg,midg; igrid,midg,midg -2.5347088E-02 3.9470039E-02 gauss-seidel spectral radius is 0.9988451 estimated iterations to convergence 233 setup time was (sec) 0.4500000 now iterating at: 03:23:51 rms-change max change #iterations 3.688569 203.5670 at 10iterations 1.825503 85.26723 at 20iterations 0.9054631 37.04588 at 30iterations 0.4499567 17.97183 at 40iterations 0.2228180 9.059371 at 50iterations 0.1115085 4.055014 at 60iterations 5.5121697E-02 2.092945 at 70iterations 2.7277442E-02 1.067314 at 80iterations 1.3577427E-02 0.5189977 at 90iterations 6.6870274E-03 0.2697430 at 100iterations 3.3473838E-03 0.1373787 at 110iterations 1.6590537E-03 6.3642502E-02 at 120iterations finished qdiffx linear iterations at : 03:23:58 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 1.6590537E-03 6.3642502E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 03:23:59 7.535u 0.205s 0:08.05 96.0% 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 03:23:59 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1121 !!! WARNING: HIT 60 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.358138 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): -6.311000 30.22800 ymin,ymax (A): 1.137000 39.96700 zmin,zma (A): -0.9830000 46.72200 x,y,z range (A): 36.53900 38.83000 47.70500 scale (grids/A): 3.358138 object centre (A): 11.95850 20.55200 22.86950 number of atom coordinates read : 1121 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.1651 centred at (gu) : 87.11611 86.79002 82.22066 assigned negative charge : -172.6512 centred at (gu) : 85.79186 86.80027 82.31794 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 103242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10838 grid for indexing accessible points = 1.400000 m= 52843 mr = 70266 m= 22138 mr = 43062 m= 6469 mr = 18167 m= 1359 mr = 5177 m= 236 mr = 1086 m= 34 mr = 176 m= 0 mr = 31 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1172 time to turn everything in is 0.7100000 number of dielectric boundary points 48356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 8488 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) : 2.238759 object centre at (A) : 11.95850 20.55200 22.86950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2012295 6.2723465E-02 midg,1,midg; midg,igrid,midg 0.3812976 0.2528727 1,midg,midg; igrid,midg,midg -0.1897405 0.2667879 gauss-seidel spectral radius is 0.9992962 estimated iterations to convergence 297 setup time was (sec) 0.9300000 now iterating at: 03:24:00 rms-change max change #iterations 8.049652 295.4955 at 10iterations 4.682352 123.9721 at 20iterations 2.718959 62.10133 at 30iterations 1.571835 35.08173 at 40iterations 0.9140903 18.98755 at 50iterations 0.5315791 11.73618 at 60iterations 0.3079467 7.328749 at 70iterations 0.1780789 3.911869 at 80iterations 0.1034469 2.172600 at 90iterations 5.9871901E-02 1.215022 at 100iterations 3.4702938E-02 0.8125134 at 110iterations 2.0199995E-02 0.4314294 at 120iterations 1.1720657E-02 0.2702980 at 130iterations 6.8066958E-03 0.1453705 at 140iterations 3.9544390E-03 9.9823475E-02 at 150iterations 2.2935644E-03 4.8236847E-02 at 160iterations 1.3297519E-03 2.8717041E-02 at 170iterations 7.7449612E-04 1.5895844E-02 at 180iterations finished qdiffx linear iterations at : 03:24:11 total time elapsed so far: 11.82000 # loops : 180 mean,max change (kT/e) : 7.7449612E-04 1.5895844E-02 energy calculations done at 11.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.95000 DelPhi exited at 03:24:11 11.950u 0.218s 0:12.46 97.5% 0+0k 0+0io 0pf+0w