Mon Oct 10 14:38:57 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 Mon Oct 10 2011 at 14:38:57 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 !!! WARNING: ASL 51 has a net charge of -0.1000 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: 0.7441939 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): 47.36700 92.24700 ymin,ymax (A): -8.938000 36.74100 zmin,zma (A): -3.637000 44.20000 x,y,z range (A): 44.88000 45.67900 47.83700 scale (grids/A): 0.7441939 object centre (A): 69.80700 13.90150 20.28150 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -5.099988 assigned positive charge : 317.9119 centred at (gu) : 89.14260 90.59039 90.19054 assigned negative charge : -323.0120 centred at (gu) : 89.15836 90.62296 90.35057 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7955 nv = 96 ne = 84 npr = 43719 no. pairs analyzed = 43719 no. exposed pairs = 2655 no. arc points = 18647 no. surface atoms = 898 nbur = 1207 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 548 mr = 4428 m= 4 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.2700000 number of dielectric boundary points 3970 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1558 ## 125 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 8416 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5109504E-08 -2.8910370E-07 midg,1,midg; midg,igrid,midg -5.5562499E-08 -1.4945525E-07 1,midg,midg; igrid,midg,midg -9.3316643E-08 -9.8813892E-08 gauss-seidel spectral radius is 0.9905885 estimated iterations to convergence 84 setup time was (sec) 0.5400000 now iterating at: 14:38:58 rms-change max change #iterations 0.2540559 31.73615 at 10iterations 3.4243327E-02 4.252470 at 20iterations 4.6027852E-03 0.6554794 at 30iterations 6.3334947E-04 8.1577301E-02 at 40iterations 8.7550798E-05 1.1367798E-02 at 50iterations finished qdiffx linear iterations at : 14:39:02 total time elapsed so far: 4.430000 # loops : 50 mean,max change (kT/e) : 8.7550798E-05 1.1367798E-02 energy calculations done at 4.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.590000 DelPhi exited at 14:39:02 4.595u 0.375s 0:05.38 92.1% 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 14:39:02 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 !!! WARNING: ASL 51 has a net charge of -0.1000 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: 2.232582 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): 47.36700 92.24700 ymin,ymax (A): -8.938000 36.74100 zmin,zma (A): -3.637000 44.20000 x,y,z range (A): 44.88000 45.67900 47.83700 scale (grids/A): 2.232582 object centre (A): 69.80700 13.90150 20.28150 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -5.099988 assigned positive charge : 317.9119 centred at (gu) : 87.42760 91.77117 90.57146 assigned negative charge : -323.0120 centred at (gu) : 87.47527 91.86902 91.05180 start vw surface at 0.1000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18647 grid for indexing accessible points = 1.400000 m= 33303 mr = 57660 m= 7049 mr = 25292 m= 717 mr = 4934 m= 17 mr = 420 m= 0 mr = 2 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 739 time to turn everything in is 0.6900000 number of dielectric boundary points 36403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 15679 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) : 0.7441939 object centre at (A) : 69.80700 13.90150 20.28150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8894597E-03 -0.1338927 midg,1,midg; midg,igrid,midg -1.8631205E-02 -3.9642092E-02 1,midg,midg; igrid,midg,midg -9.5931366E-03 2.1318337E-03 gauss-seidel spectral radius is 0.9989337 estimated iterations to convergence 242 setup time was (sec) 1.010000 now iterating at: 14:39:04 rms-change max change #iterations 5.176114 211.2156 at 10iterations 2.626098 93.17300 at 20iterations 1.343203 39.82111 at 30iterations 0.6880809 19.34362 at 40iterations 0.3506350 12.10567 at 50iterations 0.1791759 4.962769 at 60iterations 9.1329686E-02 2.868553 at 70iterations 4.6837881E-02 1.304166 at 80iterations 2.3876397E-02 0.7792910 at 90iterations 1.2251968E-02 0.3378930 at 100iterations 6.2510311E-03 0.1723385 at 110iterations 3.1885004E-03 9.2226028E-02 at 120iterations finished qdiffx linear iterations at : 14:39:14 total time elapsed so far: 11.70000 # loops : 120 mean,max change (kT/e) : 3.1885004E-03 9.2226028E-02 energy calculations done at 11.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.86000 DelPhi exited at 14:39:15 11.869u 0.439s 0:12.66 97.0% 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 14:39:15 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 !!! WARNING: ASL 51 has a net charge of -0.1000 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: 3.348872 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): 47.36700 92.24700 ymin,ymax (A): -8.938000 36.74100 zmin,zma (A): -3.637000 44.20000 x,y,z range (A): 44.88000 45.67900 47.83700 scale (grids/A): 3.348872 object centre (A): 69.80700 13.90150 20.28150 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -5.099988 assigned positive charge : 317.9119 centred at (gu) : 86.14147 92.65678 90.85719 assigned negative charge : -323.0120 centred at (gu) : 86.21286 92.80356 91.57774 start vw surface at 0.1100000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 192775 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18647 grid for indexing accessible points = 1.400000 m= 102496 mr = 139266 m= 43599 mr = 84887 m= 13550 mr = 36231 m= 2908 mr = 10777 m= 403 mr = 2289 m= 17 mr = 272 m= 0 mr = 11 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 2539 time to turn everything in is 2.220000 number of dielectric boundary points 82015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.380000 number of grid points assigned charge 15736 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) : 2.232582 object centre at (A) : 69.80700 13.90150 20.28150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1539095 -1.532691 midg,1,midg; midg,igrid,midg -0.1469377 -0.2570837 1,midg,midg; igrid,midg,midg -2.4644015E-02 1.0272034E-02 gauss-seidel spectral radius is 0.9993219 estimated iterations to convergence 303 setup time was (sec) 2.590000 now iterating at: 14:39:18 rms-change max change #iterations 11.15952 285.8946 at 10iterations 6.576009 134.0707 at 20iterations 3.888004 63.18064 at 30iterations 2.286411 37.49723 at 40iterations 1.348583 20.85805 at 50iterations 0.7933356 13.87207 at 60iterations 0.4666087 7.234815 at 70iterations 0.2747266 4.479578 at 80iterations 0.1615120 2.668175 at 90iterations 9.4880015E-02 1.586169 at 100iterations 5.5795595E-02 0.8691835 at 110iterations 3.2690007E-02 0.5231094 at 120iterations 1.9297421E-02 0.3018494 at 130iterations 1.1321067E-02 0.1769695 at 140iterations 6.6608316E-03 0.1075287 at 150iterations 3.9195893E-03 6.0587704E-02 at 160iterations 2.3023221E-03 3.6101580E-02 at 170iterations 1.3542750E-03 2.1644592E-02 at 180iterations finished qdiffx linear iterations at : 14:39:35 total time elapsed so far: 19.79000 # loops : 180 mean,max change (kT/e) : 1.3542750E-03 2.1644592E-02 energy calculations done at 19.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.96000 DelPhi exited at 14:39:36 19.961u 0.452s 0:21.13 96.5% 0+0k 0+0io 0pf+0w