Tue Oct 11 05:30:16 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 Tue Oct 11 2011 at 05:30:16 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2277 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: SEP 177 has a net charge of -0.4750 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: 0.6866357 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): 19.77000 63.16300 ymin,ymax (A): -3.556000 33.71800 zmin,zma (A): 20.02400 71.87100 x,y,z range (A): 43.39300 37.27400 51.84700 scale (grids/A): 0.6866357 object centre (A): 41.46650 15.08100 45.94750 number of atom coordinates read : 2277 total number of charged atoms : 1953 net assigned charge : 5.564011 assigned positive charge : 317.4261 centred at (gu) : 90.02145 89.62808 89.20900 assigned negative charge : -311.8622 centred at (gu) : 90.16737 89.66266 89.17086 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6685 nv = 96 ne = 84 npr = 41670 no. pairs analyzed = 41670 no. exposed pairs = 2553 no. arc points = 17324 no. surface atoms = 871 nbur = 1406 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 399 mr = 3851 m= 2 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1685 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7527 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9303050E-08 3.4288366E-08 midg,1,midg; midg,igrid,midg 4.1907025E-08 1.6579543E-08 1,midg,midg; igrid,midg,midg 7.2117189E-08 -1.7059758E-08 gauss-seidel spectral radius is 0.9889494 estimated iterations to convergence 78 setup time was (sec) 0.3500000 now iterating at: 05:30:17 rms-change max change #iterations 0.1753856 26.45732 at 10iterations 2.0980664E-02 2.956036 at 20iterations 2.7566880E-03 0.3774748 at 30iterations 5.0608133E-04 6.2465668E-02 at 40iterations 1.3785220E-04 1.7030716E-02 at 50iterations finished qdiffx linear iterations at : 05:30:20 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.3785220E-04 1.7030716E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 05:30:20 3.333u 0.188s 0:03.89 90.2% 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 05:30:20 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2277 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: SEP 177 has a net charge of -0.4750 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: 2.059907 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): 19.77000 63.16300 ymin,ymax (A): -3.556000 33.71800 zmin,zma (A): 20.02400 71.87100 x,y,z range (A): 43.39300 37.27400 51.84700 scale (grids/A): 2.059907 object centre (A): 41.46650 15.08100 45.94750 number of atom coordinates read : 2277 total number of charged atoms : 1953 net assigned charge : 5.564011 assigned positive charge : 317.4261 centred at (gu) : 90.06444 88.88427 87.62704 assigned negative charge : -311.8622 centred at (gu) : 90.50217 88.98804 87.51248 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71119 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17324 grid for indexing accessible points = 1.400000 m= 28607 mr = 50597 m= 5423 mr = 21815 m= 450 mr = 3606 m= 7 mr = 214 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 29374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15474 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) : 0.6866357 object centre at (A) : 41.46650 15.08100 45.94750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6116985E-02 3.2376911E-02 midg,1,midg; midg,igrid,midg 2.0625103E-02 6.4665754E-03 1,midg,midg; igrid,midg,midg 2.9492788E-02 6.7259558E-03 gauss-seidel spectral radius is 0.9987673 estimated iterations to convergence 226 setup time was (sec) 0.5700000 now iterating at: 05:30:21 rms-change max change #iterations 4.383402 176.6647 at 10iterations 2.138990 71.53963 at 20iterations 1.040770 43.79000 at 30iterations 0.5108819 17.74699 at 40iterations 0.2489915 9.522281 at 50iterations 0.1213193 3.659058 at 60iterations 5.9266914E-02 1.724617 at 70iterations 2.8998747E-02 0.9265251 at 80iterations 1.4295527E-02 0.4416752 at 90iterations 7.0649385E-03 0.2306023 at 100iterations 3.5371867E-03 0.1076355 at 110iterations 1.8368582E-03 6.2996149E-02 at 120iterations finished qdiffx linear iterations at : 05:30:28 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 1.8368582E-03 6.2996149E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 05:30:29 7.733u 0.204s 0:08.48 93.5% 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 05:30:29 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2277 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: SEP 177 has a net charge of -0.4750 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: 3.089860 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): 19.77000 63.16300 ymin,ymax (A): -3.556000 33.71800 zmin,zma (A): 20.02400 71.87100 x,y,z range (A): 43.39300 37.27400 51.84700 scale (grids/A): 3.089860 object centre (A): 41.46650 15.08100 45.94750 number of atom coordinates read : 2277 total number of charged atoms : 1953 net assigned charge : 5.564011 assigned positive charge : 317.4261 centred at (gu) : 90.09653 88.32639 86.44061 assigned negative charge : -311.8622 centred at (gu) : 90.75333 88.48215 86.26883 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 163996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17324 grid for indexing accessible points = 1.400000 m= 89509 mr = 121727 m= 36050 mr = 74729 m= 10261 mr = 29772 m= 1893 mr = 7948 m= 193 mr = 1389 m= 5 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.090000 number of dielectric boundary points 66218 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 15623 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) : 2.059907 object centre at (A) : 41.46650 15.08100 45.94750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4294039 0.2522810 midg,1,midg; midg,igrid,midg 0.1847219 5.1928520E-02 1,midg,midg; igrid,midg,midg 0.2659600 0.2092459 gauss-seidel spectral radius is 0.9992785 estimated iterations to convergence 294 setup time was (sec) 1.340000 now iterating at: 05:30:30 rms-change max change #iterations 9.919214 345.9749 at 10iterations 5.862793 169.7414 at 20iterations 3.452023 78.33040 at 30iterations 2.023660 48.23420 at 40iterations 1.183720 28.17505 at 50iterations 0.6923992 14.72506 at 60iterations 0.4043054 7.456048 at 70iterations 0.2353766 5.170490 at 80iterations 0.1373751 2.440105 at 90iterations 8.0099657E-02 1.406455 at 100iterations 4.6760187E-02 0.9343035 at 110iterations 2.7311411E-02 0.5481567 at 120iterations 1.6090287E-02 0.2860565 at 130iterations 9.5366174E-03 0.1822281 at 140iterations 5.7661645E-03 0.1083183 at 150iterations 3.5942695E-03 6.1670303E-02 at 160iterations 2.3712786E-03 4.4784546E-02 at 170iterations 1.6494013E-03 3.0128479E-02 at 180iterations finished qdiffx linear iterations at : 05:30:41 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 1.6494013E-03 3.0128479E-02 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.61000 DelPhi exited at 05:30:42 12.609u 0.191s 0:13.24 96.6% 0+0k 0+0io 0pf+0w