Tue Nov 22 14:13:04 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+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 Nov 22 2011 at 14:13:10 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6308030 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): -35.18300 9.982000 ymin,ymax (A): 1.087000 41.64500 zmin,zma (A): -1.181000 55.25500 x,y,z range (A): 45.16500 40.55800 56.43600 scale (grids/A): 0.6308030 object centre (A): -12.60050 21.36600 27.03700 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000007 assigned positive charge : 291.4719 centred at (gu) : 90.43779 89.47153 90.53342 assigned negative charge : -286.4722 centred at (gu) : 90.40804 89.52123 90.55830 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5212 nv = 96 ne = 84 npr = 40631 no. pairs analyzed = 40631 no. exposed pairs = 2498 no. arc points = 17210 no. surface atoms = 844 nbur = 1122 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 260 mr = 2868 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1666 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 6230 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4363839E-09 4.3312669E-09 midg,1,midg; midg,igrid,midg 9.9107069E-09 1.9988242E-09 1,midg,midg; igrid,midg,midg 3.2544587E-09 8.2636245E-09 gauss-seidel spectral radius is 0.9869260 estimated iterations to convergence 72 setup time was (sec) 0.4300000 now iterating at: 14:13:13 rms-change max change #iterations 0.1204679 20.68443 at 10iterations 1.1395451E-02 2.218394 at 20iterations 1.0812890E-03 0.1954498 at 30iterations 1.0233833E-04 1.5903950E-02 at 40iterations 9.7969241E-06 1.4667511E-03 at 50iterations finished qdiffx linear iterations at : 14:13:21 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 9.7969241E-06 1.4667511E-03 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 14:13:23 3.045u 0.133s 0:14.20 22.3% 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 Nov 22 2011 at 14:13:25 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.892409 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): -35.18300 9.982000 ymin,ymax (A): 1.087000 41.64500 zmin,zma (A): -1.181000 55.25500 x,y,z range (A): 45.16500 40.55800 56.43600 scale (grids/A): 1.892409 object centre (A): -12.60050 21.36600 27.03700 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000007 assigned positive charge : 291.4719 centred at (gu) : 91.31328 88.41466 91.59992 assigned negative charge : -286.4722 centred at (gu) : 91.22430 88.56395 91.67488 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 56564 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17210 grid for indexing accessible points = 1.400000 m= 20667 mr = 38921 m= 3149 mr = 15555 m= 151 mr = 2035 m= 1 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 794 time to turn everything in is 0.4000000 number of dielectric boundary points 23958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 14424 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) : 0.6308030 object centre at (A) : -12.60050 21.36600 27.03700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8963106E-02 3.7192240E-02 midg,1,midg; midg,igrid,midg 2.4478836E-03 3.5291689E-03 1,midg,midg; igrid,midg,midg -1.2213709E-04 -2.1753060E-03 gauss-seidel spectral radius is 0.9985406 estimated iterations to convergence 208 setup time was (sec) 0.6700000 now iterating at: 14:13:30 rms-change max change #iterations 3.532945 163.9289 at 10iterations 1.617517 64.50750 at 20iterations 0.7383220 28.58990 at 30iterations 0.3380469 12.85329 at 40iterations 0.1532137 6.458179 at 50iterations 7.0147552E-02 2.375226 at 60iterations 3.2078337E-02 1.160633 at 70iterations 1.4549844E-02 0.5041237 at 80iterations 6.6750892E-03 0.2213607 at 90iterations 3.0392897E-03 0.1089554 at 100iterations 1.3839450E-03 4.8345566E-02 at 110iterations 6.3501386E-04 2.1486759E-02 at 120iterations finished qdiffx linear iterations at : 14:13:48 total time elapsed so far: 6.760000 # loops : 120 mean,max change (kT/e) : 6.3501386E-04 2.1486759E-02 energy calculations done at 6.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 14:13:59 6.926u 0.185s 0:34.40 20.6% 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 Nov 22 2011 at 14:14:04 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.838614 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): -35.18300 9.982000 ymin,ymax (A): 1.087000 41.64500 zmin,zma (A): -1.181000 55.25500 x,y,z range (A): 45.16500 40.55800 56.43600 scale (grids/A): 2.838614 object centre (A): -12.60050 21.36600 27.03700 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000007 assigned positive charge : 291.4719 centred at (gu) : 91.96983 87.62197 92.39999 assigned negative charge : -286.4722 centred at (gu) : 91.83639 87.84595 92.51247 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 130646 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17210 grid for indexing accessible points = 1.400000 m= 66743 mr = 94087 m= 24487 mr = 55195 m= 5557 mr = 20237 m= 624 mr = 4207 m= 40 mr = 452 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 2735 time to turn everything in is 1.020000 number of dielectric boundary points 53901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 14672 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) : 1.892409 object centre at (A) : -12.60050 21.36600 27.03700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1656046 0.2780750 midg,1,midg; midg,igrid,midg -4.9332604E-02 2.9370405E-02 1,midg,midg; igrid,midg,midg -3.3722423E-02 -6.2785588E-02 gauss-seidel spectral radius is 0.9992152 estimated iterations to convergence 282 setup time was (sec) 1.320000 now iterating at: 14:14:13 rms-change max change #iterations 8.438198 473.4603 at 10iterations 4.862799 120.6435 at 20iterations 2.766205 59.24207 at 30iterations 1.571863 36.68248 at 40iterations 0.8895493 19.01548 at 50iterations 0.5034219 11.06470 at 60iterations 0.2846259 6.939672 at 70iterations 0.1611376 3.556446 at 80iterations 9.0856329E-02 1.983806 at 90iterations 5.1322605E-02 1.011077 at 100iterations 2.8963225E-02 0.5813141 at 110iterations 1.6362799E-02 0.3401299 at 120iterations 9.2220232E-03 0.1746931 at 130iterations 5.2012596E-03 0.1036394 at 140iterations 2.9419770E-03 6.2376022E-02 at 150iterations 1.6544808E-03 3.2538176E-02 at 160iterations 9.3295990E-04 2.0737648E-02 at 170iterations 5.2677025E-04 1.1501312E-02 at 180iterations finished qdiffx linear iterations at : 14:14:42 total time elapsed so far: 10.96000 # loops : 180 mean,max change (kT/e) : 5.2677025E-04 1.1501312E-02 energy calculations done at 10.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.13000 DelPhi exited at 14:14:44 11.136u 0.214s 0:40.77 27.8% 0+0k 0+0io 0pf+0w