Tue Oct 11 03:44:36 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 Tue Oct 11 2011 at 03:44:36 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 = 2940 !!! WARNING: GLN 307 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6000033 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): -12.08400 36.80200 ymin,ymax (A): 3.484000 51.94900 zmin,zma (A): -13.63700 45.69600 x,y,z range (A): 48.88600 48.46500 59.33300 scale (grids/A): 0.6000033 object centre (A): 12.35900 27.71650 16.02950 number of atom coordinates read : 2940 total number of charged atoms : 2789 net assigned charge : 3.728029 assigned positive charge : 447.1134 centred at (gu) : 90.12927 89.95975 92.14702 assigned negative charge : -443.3861 centred at (gu) : 89.92234 89.79338 92.08407 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6919 nv = 96 ne = 84 npr = 59745 no. pairs analyzed = 59745 no. exposed pairs = 3516 no. arc points = 24506 no. surface atoms = 1188 nbur = 1752 mkacc time = 0.2200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 326 mr = 3871 m= 4 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.4500000 number of dielectric boundary points 3356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2469 ## 289 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 8668 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4740963E-10 6.7583130E-09 midg,1,midg; midg,igrid,midg -5.5561205E-09 8.2299447E-09 1,midg,midg; igrid,midg,midg -7.0446853E-09 1.0216246E-08 gauss-seidel spectral radius is 0.9856460 estimated iterations to convergence 68 setup time was (sec) 0.7400000 now iterating at: 03:44:37 rms-change max change #iterations 0.1181568 17.72639 at 10iterations 1.0335748E-02 1.930740 at 20iterations 1.2933094E-03 0.2014904 at 30iterations 4.2040570E-04 8.0627441E-02 at 40iterations 1.8786758E-04 3.6027908E-02 at 50iterations finished qdiffx linear iterations at : 03:44:40 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 1.8786758E-04 3.6027908E-02 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.300000 DelPhi exited at 03:44:41 4.299u 0.171s 0:05.02 88.8% 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 Tue Oct 11 2011 at 03:44:41 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 = 2940 !!! WARNING: GLN 307 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.800010 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): -12.08400 36.80200 ymin,ymax (A): 3.484000 51.94900 zmin,zma (A): -13.63700 45.69600 x,y,z range (A): 48.88600 48.46500 59.33300 scale (grids/A): 1.800010 object centre (A): 12.35900 27.71650 16.02950 number of atom coordinates read : 2940 total number of charged atoms : 2789 net assigned charge : 3.728029 assigned positive charge : 447.1134 centred at (gu) : 90.38715 89.87868 96.44042 assigned negative charge : -443.3861 centred at (gu) : 89.76654 89.37984 96.25184 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 75665 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24506 grid for indexing accessible points = 1.400000 m= 26032 mr = 53306 m= 3469 mr = 19068 m= 120 mr = 1968 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 160 time to turn everything in is 0.6900000 number of dielectric boundary points 30923 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 224 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 21745 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) : 0.6000033 object centre at (A) : 12.35900 27.71650 16.02950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6044216E-02 1.0307311E-03 midg,1,midg; midg,igrid,midg -5.9048999E-03 2.0585274E-02 1,midg,midg; igrid,midg,midg -4.3207048E-03 3.6381673E-02 gauss-seidel spectral radius is 0.9985066 estimated iterations to convergence 205 setup time was (sec) 1.030000 now iterating at: 03:44:42 rms-change max change #iterations 4.107872 177.8214 at 10iterations 1.854371 66.36790 at 20iterations 0.8389583 27.09178 at 30iterations 0.3805234 11.59185 at 40iterations 0.1725868 5.749619 at 50iterations 7.8607246E-02 2.568535 at 60iterations 3.5562418E-02 1.081402 at 70iterations 1.6213454E-02 0.6037865 at 80iterations 7.4434672E-03 0.2422409 at 90iterations 3.5005426E-03 0.1158333 at 100iterations 1.7276544E-03 6.0853958E-02 at 110iterations 9.3912357E-04 3.7921906E-02 at 120iterations finished qdiffx linear iterations at : 03:44:50 total time elapsed so far: 9.450000 # loops : 120 mean,max change (kT/e) : 9.3912357E-04 3.7921906E-02 energy calculations done at 9.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.690000 DelPhi exited at 03:44:51 9.690u 0.193s 0:10.61 93.1% 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 Tue Oct 11 2011 at 03:44:51 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 = 2940 !!! WARNING: GLN 307 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.700015 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): -12.08400 36.80200 ymin,ymax (A): 3.484000 51.94900 zmin,zma (A): -13.63700 45.69600 x,y,z range (A): 48.88600 48.46500 59.33300 scale (grids/A): 2.700015 object centre (A): 12.35900 27.71650 16.02950 number of atom coordinates read : 2940 total number of charged atoms : 2789 net assigned charge : 3.728029 assigned positive charge : 447.1134 centred at (gu) : 90.58054 89.81801 99.66036 assigned negative charge : -443.3861 centred at (gu) : 89.64976 89.06970 99.37780 start vw surface at 0.2300000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 175011 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24506 grid for indexing accessible points = 1.400000 m= 87181 mr = 128974 m= 28794 mr = 71390 m= 5890 mr = 22805 m= 630 mr = 4226 m= 22 mr = 323 m= 0 mr = 1 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 553 time to turn everything in is 1.730000 number of dielectric boundary points 69809 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 22308 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) : 1.800010 object centre at (A) : 12.35900 27.71650 16.02950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.244320 0.1728858 midg,1,midg; midg,igrid,midg -7.7517688E-02 0.2412098 1,midg,midg; igrid,midg,midg -4.9462534E-02 0.3572860 gauss-seidel spectral radius is 0.9992257 estimated iterations to convergence 284 setup time was (sec) 2.080000 now iterating at: 03:44:54 rms-change max change #iterations 9.946830 298.4339 at 10iterations 5.806977 163.5260 at 20iterations 3.363099 91.47889 at 30iterations 1.941257 39.00302 at 40iterations 1.115652 23.62080 at 50iterations 0.6409892 13.68144 at 60iterations 0.3671123 8.331238 at 70iterations 0.2099720 4.147570 at 80iterations 0.1197936 2.407409 at 90iterations 6.8383709E-02 1.389371 at 100iterations 3.9133273E-02 0.7620440 at 110iterations 2.2263912E-02 0.4742260 at 120iterations 1.2767534E-02 0.2810755 at 130iterations 7.3497919E-03 0.1673985 at 140iterations 4.2571835E-03 7.9156280E-02 at 150iterations 2.5195063E-03 5.1414490E-02 at 160iterations 1.5402262E-03 3.4463882E-02 at 170iterations 9.9788350E-04 2.1230698E-02 at 180iterations finished qdiffx linear iterations at : 03:45:06 total time elapsed so far: 14.05000 # loops : 180 mean,max change (kT/e) : 9.9788350E-04 2.1230698E-02 energy calculations done at 14.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.27000 DelPhi exited at 03:45:07 14.276u 0.196s 0:15.08 95.8% 0+0k 0+0io 0pf+0w