Mon Oct 10 23:15:51 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 Mon Oct 10 2011 at 23:15:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2647 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: 0.6360323 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): -19.88900 30.63300 ymin,ymax (A): 17.59000 73.56200 zmin,zma (A): 9.662001 51.86300 x,y,z range (A): 50.52200 55.97200 42.20100 scale (grids/A): 0.6360323 object centre (A): 5.372000 45.57600 30.76250 number of atom coordinates read : 2647 total number of charged atoms : 2506 net assigned charge : 5.500021 assigned positive charge : 398.1997 centred at (gu) : 91.58345 90.10280 89.85228 assigned negative charge : -392.7004 centred at (gu) : 91.58426 90.32820 90.04832 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7017 nv = 96 ne = 84 npr = 53893 no. pairs analyzed = 53893 no. exposed pairs = 3083 no. arc points = 21470 no. surface atoms = 1048 nbur = 1599 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 341 mr = 4000 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 119 time to turn everything in is 0.3000000 number of dielectric boundary points 3315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2054 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8511 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8324411E-08 -1.3527322E-08 midg,1,midg; midg,igrid,midg 2.9725678E-08 -1.7637502E-08 1,midg,midg; igrid,midg,midg 5.2354281E-09 9.8719095E-09 gauss-seidel spectral radius is 0.9871937 estimated iterations to convergence 72 setup time was (sec) 0.5300000 now iterating at: 23:15:52 rms-change max change #iterations 0.1461002 20.52868 at 10iterations 1.4569018E-02 2.127609 at 20iterations 2.0597510E-03 0.4051094 at 30iterations 5.1040243E-04 0.1207771 at 40iterations 1.6424077E-04 3.9768219E-02 at 50iterations finished qdiffx linear iterations at : 23:15:55 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 1.6424077E-04 3.9768219E-02 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 23:15:55 3.267u 0.189s 0:03.89 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 23:15:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2647 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: 1.908097 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): -19.88900 30.63300 ymin,ymax (A): 17.59000 73.56200 zmin,zma (A): 9.662001 51.86300 x,y,z range (A): 50.52200 55.97200 42.20100 scale (grids/A): 1.908097 object centre (A): 5.372000 45.57600 30.76250 number of atom coordinates read : 2647 total number of charged atoms : 2506 net assigned charge : 5.500021 assigned positive charge : 398.1997 centred at (gu) : 94.74975 90.30775 89.55647 assigned negative charge : -392.7004 centred at (gu) : 94.75230 90.98421 90.14487 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21470 grid for indexing accessible points = 1.400000 m= 27389 mr = 54240 m= 4207 mr = 20459 m= 247 mr = 2829 m= 4 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 4682 time to turn everything in is 0.5300000 number of dielectric boundary points 30821 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19713 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) : 0.6360323 object centre at (A) : 5.372000 45.57600 30.76250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6420964E-02 3.9974097E-03 midg,1,midg; midg,igrid,midg -1.4949596E-02 -2.6917007E-02 1,midg,midg; igrid,midg,midg 1.8560143E-02 1.9080637E-03 gauss-seidel spectral radius is 0.9986378 estimated iterations to convergence 215 setup time was (sec) 0.8000000 now iterating at: 23:15:56 rms-change max change #iterations 4.245042 184.5561 at 10iterations 1.980967 63.11745 at 20iterations 0.9295815 28.06021 at 30iterations 0.4371960 13.71023 at 40iterations 0.2049940 6.405605 at 50iterations 9.5956556E-02 3.095627 at 60iterations 4.5128834E-02 1.540478 at 70iterations 2.1430938E-02 0.6609364 at 80iterations 1.0161242E-02 0.3167114 at 90iterations 4.8517631E-03 0.1657829 at 100iterations 2.3883884E-03 9.3214989E-02 at 110iterations 1.2373524E-03 4.6028137E-02 at 120iterations finished qdiffx linear iterations at : 23:16:03 total time elapsed so far: 7.220000 # loops : 120 mean,max change (kT/e) : 1.2373524E-03 4.6028137E-02 energy calculations done at 7.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.400000 DelPhi exited at 23:16:03 7.403u 0.154s 0:07.94 95.0% 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 Mon Oct 10 2011 at 23:16:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2647 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: 2.862145 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): -19.88900 30.63300 ymin,ymax (A): 17.59000 73.56200 zmin,zma (A): 9.662001 51.86300 x,y,z range (A): 50.52200 55.97200 42.20100 scale (grids/A): 2.862145 object centre (A): 5.372000 45.57600 30.76250 number of atom coordinates read : 2647 total number of charged atoms : 2506 net assigned charge : 5.500021 assigned positive charge : 398.1997 centred at (gu) : 97.12447 90.46159 89.33448 assigned negative charge : -392.7004 centred at (gu) : 97.12839 91.47623 90.21721 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 177632 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21470 grid for indexing accessible points = 1.400000 m= 89086 mr = 131270 m= 31699 mr = 73857 m= 7688 mr = 25856 m= 1031 mr = 5956 m= 42 mr = 733 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.7599999 no. cavity mid-points inaccessible to solvent = 15572 time to turn everything in is 1.340000 number of dielectric boundary points 69499 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 20048 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) : 1.908097 object centre at (A) : 5.372000 45.57600 30.76250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3353423 9.2941217E-02 midg,1,midg; midg,igrid,midg -0.5888114 -0.2479922 1,midg,midg; igrid,midg,midg 0.1644945 -4.6564443E-03 gauss-seidel spectral radius is 0.9992542 estimated iterations to convergence 289 setup time was (sec) 1.640000 now iterating at: 23:16:05 rms-change max change #iterations 9.880327 436.3071 at 10iterations 5.694839 134.2950 at 20iterations 3.275605 59.60362 at 30iterations 1.882850 33.97847 at 40iterations 1.083150 19.99304 at 50iterations 0.6197070 11.59786 at 60iterations 0.3558332 6.096878 at 70iterations 0.2038948 4.062717 at 80iterations 0.1170016 2.001602 at 90iterations 6.7083575E-02 1.151262 at 100iterations 3.8436089E-02 0.7238357 at 110iterations 2.2090374E-02 0.3799906 at 120iterations 1.2714370E-02 0.2249336 at 130iterations 7.3260991E-03 0.1363583 at 140iterations 4.2491141E-03 8.1874847E-02 at 150iterations 2.4920127E-03 4.5253754E-02 at 160iterations 1.4950751E-03 3.2238007E-02 at 170iterations 9.3244994E-04 2.1427155E-02 at 180iterations finished qdiffx linear iterations at : 23:16:15 total time elapsed so far: 11.92000 # loops : 180 mean,max change (kT/e) : 9.3244994E-04 2.1427155E-02 energy calculations done at 11.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.09000 DelPhi exited at 23:16:16 12.091u 0.230s 0:12.73 96.7% 0+0k 0+0io 0pf+0w