Sun Oct 9 19:43:50 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 Sun Oct 9 2011 at 19:43:51 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4880 !!! WARNING: PLP 999 has a net charge of 0.2320 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5692720 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): 3.220000 64.41500 ymin,ymax (A): -8.592999 53.40900 zmin,zma (A): -1.145000 61.39100 x,y,z range (A): 61.19500 62.00200 62.53600 scale (grids/A): 0.5692720 object centre (A): 33.81750 22.40800 30.12300 number of atom coordinates read : 4880 total number of charged atoms : 4723 net assigned charge : 2.232040 assigned positive charge : 742.9304 centred at (gu) : 88.27569 89.11002 89.17748 assigned negative charge : -740.7036 centred at (gu) : 88.14890 89.13100 89.13937 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 10439 nv = 96 ne = 84 npr = 99264 no. pairs analyzed = 99264 no. exposed pairs = 5715 no. arc points = 38824 no. surface atoms = 1936 nbur = 2944 mkacc time = 0.1700000 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= 502 mr = 6049 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4855 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3919 ## 404 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 13452 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0367201E-10 1.1203148E-09 midg,1,midg; midg,igrid,midg 1.1522571E-09 -1.0563195E-10 1,midg,midg; igrid,midg,midg -4.3907877E-09 2.3653695E-09 gauss-seidel spectral radius is 0.9842195 estimated iterations to convergence 65 setup time was (sec) 0.5200000 now iterating at: 19:43:51 rms-change max change #iterations 0.1235279 13.78223 at 10iterations 1.3618738E-02 2.121323 at 20iterations 4.3710629E-03 0.5317459 at 30iterations 1.8948835E-03 0.2237244 at 40iterations 8.5181469E-04 9.8495483E-02 at 50iterations finished qdiffx linear iterations at : 19:43:54 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 8.5181469E-04 9.8495483E-02 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 19:43:55 3.588u 0.179s 0:04.04 92.8% 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 Sun Oct 9 2011 at 19:43:55 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4880 !!! WARNING: PLP 999 has a net charge of 0.2320 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.707816 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): 3.220000 64.41500 ymin,ymax (A): -8.592999 53.40900 zmin,zma (A): -1.145000 61.39100 x,y,z range (A): 61.19500 62.00200 62.53600 scale (grids/A): 1.707816 object centre (A): 33.81750 22.40800 30.12300 number of atom coordinates read : 4880 total number of charged atoms : 4723 net assigned charge : 2.232040 assigned positive charge : 742.9304 centred at (gu) : 84.82571 87.32837 87.53082 assigned negative charge : -740.7036 centred at (gu) : 84.44663 87.39297 87.41814 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 115711 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38824 grid for indexing accessible points = 1.400000 m= 41381 mr = 84328 m= 5432 mr = 30278 m= 218 mr = 3042 m= 0 mr = 44 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 45050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 319 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 36510 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) : 0.5692720 object centre at (A) : 33.81750 22.40800 30.12300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5787245E-02 -4.5068539E-03 midg,1,midg; midg,igrid,midg 1.9162364E-02 9.9897003E-03 1,midg,midg; igrid,midg,midg -1.7720591E-02 4.3471277E-02 gauss-seidel spectral radius is 0.9985174 estimated iterations to convergence 206 setup time was (sec) 0.7700000 now iterating at: 19:43:56 rms-change max change #iterations 4.976624 203.9161 at 10iterations 2.255768 69.85957 at 20iterations 1.023694 28.49476 at 30iterations 0.4671037 13.33783 at 40iterations 0.2131122 5.795972 at 50iterations 9.7802207E-02 2.651672 at 60iterations 4.5768611E-02 1.377556 at 70iterations 2.1943096E-02 0.5982094 at 80iterations 1.1356543E-02 0.3206406 at 90iterations 6.5528210E-03 0.1947651 at 100iterations 4.2138738E-03 0.1080170 at 110iterations 2.9319050E-03 7.0098877E-02 at 120iterations finished qdiffx linear iterations at : 19:44:03 total time elapsed so far: 8.180000 # loops : 120 mean,max change (kT/e) : 2.9319050E-03 7.0098877E-02 energy calculations done at 8.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.300000 DelPhi exited at 19:44:03 8.304u 0.220s 0:08.80 96.8% 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 Sun Oct 9 2011 at 19:44:03 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 = 4880 !!! WARNING: PLP 999 has a net charge of 0.2320 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.561724 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): 3.220000 64.41500 ymin,ymax (A): -8.592999 53.40900 zmin,zma (A): -1.145000 61.39100 x,y,z range (A): 61.19500 62.00200 62.53600 scale (grids/A): 2.561724 object centre (A): 33.81750 22.40800 30.12300 number of atom coordinates read : 4880 total number of charged atoms : 4723 net assigned charge : 2.232040 assigned positive charge : 742.9304 centred at (gu) : 82.23808 85.99228 86.29593 assigned negative charge : -740.7036 centred at (gu) : 81.67001 86.08944 86.12721 start vw surface at 0.1300000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 268701 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38824 grid for indexing accessible points = 1.400000 m= 138282 mr = 204744 m= 45814 mr = 113399 m= 9295 mr = 36162 m= 966 mr = 6654 m= 30 mr = 531 m= 0 mr = 8 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.430000 number of dielectric boundary points 101590 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 37752 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) : 1.707816 object centre at (A) : 33.81750 22.40800 30.12300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4602252 4.3427765E-02 midg,1,midg; midg,igrid,midg -3.2401573E-02 6.1776564E-03 1,midg,midg; igrid,midg,midg -0.3693183 0.6416686 gauss-seidel spectral radius is 0.9992737 estimated iterations to convergence 293 setup time was (sec) 1.690000 now iterating at: 19:44:05 rms-change max change #iterations 12.42798 308.1145 at 10iterations 7.377392 160.4244 at 20iterations 4.340034 79.68194 at 30iterations 2.548498 43.68752 at 40iterations 1.491028 23.08202 at 50iterations 0.8711819 15.15359 at 60iterations 0.5073787 7.865204 at 70iterations 0.2954014 4.791908 at 80iterations 0.1717089 2.664795 at 90iterations 9.9969178E-02 1.509968 at 100iterations 5.8368724E-02 0.8962860 at 110iterations 3.4213319E-02 0.5724626 at 120iterations 2.0326387E-02 0.3209991 at 130iterations 1.2346286E-02 0.2286682 at 140iterations 7.7691437E-03 0.1308441 at 150iterations 5.1858579E-03 8.2443237E-02 at 160iterations 3.6813156E-03 5.7357788E-02 at 170iterations 2.7825059E-03 4.1748047E-02 at 180iterations finished qdiffx linear iterations at : 19:44:17 total time elapsed so far: 13.67000 # loops : 180 mean,max change (kT/e) : 2.7825059E-03 4.1748047E-02 energy calculations done at 13.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.80000 DelPhi exited at 19:44:18 13.806u 0.192s 0:14.27 98.0% 0+0k 0+0io 0pf+0w