Tue Oct 11 08:32:44 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 08:32:44 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2081 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: GLM 174 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7198318 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): -20.75200 26.53600 ymin,ymax (A): -10.84000 26.15200 zmin,zma (A): -3.172000 46.28400 x,y,z range (A): 47.28800 36.99200 49.45600 scale (grids/A): 0.7198318 object centre (A): 2.892001 7.656001 21.55600 number of atom coordinates read : 2081 total number of charged atoms : 1947 net assigned charge : 5.945010 assigned positive charge : 317.6060 centred at (gu) : 89.24409 89.23904 90.85811 assigned negative charge : -311.6611 centred at (gu) : 89.08864 89.26670 90.92039 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7358 nv = 96 ne = 84 npr = 41982 no. pairs analyzed = 41982 no. exposed pairs = 2523 no. arc points = 17430 no. surface atoms = 864 nbur = 1217 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 513 mr = 4293 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1529 ## 130 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7988 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1914103E-08 3.1702704E-08 midg,1,midg; midg,igrid,midg 9.9056557E-08 4.3637765E-08 1,midg,midg; igrid,midg,midg -4.0360909E-08 1.4458578E-07 gauss-seidel spectral radius is 0.9899357 estimated iterations to convergence 81 setup time was (sec) 0.5000000 now iterating at: 08:32:45 rms-change max change #iterations 0.2182679 29.15937 at 10iterations 2.8231999E-02 4.118841 at 20iterations 3.7453065E-03 0.4775915 at 30iterations 5.7458470E-04 7.3646545E-02 at 40iterations 1.2163064E-04 1.5266418E-02 at 50iterations finished qdiffx linear iterations at : 08:32:47 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 1.2163064E-04 1.5266418E-02 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 08:32:48 3.128u 0.138s 0:03.60 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 08:32:48 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2081 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: GLM 174 has a net charge of -0.0940 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: 2.159495 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): -20.75200 26.53600 ymin,ymax (A): -10.84000 26.15200 zmin,zma (A): -3.172000 46.28400 x,y,z range (A): 47.28800 36.99200 49.45600 scale (grids/A): 2.159495 object centre (A): 2.892001 7.656001 21.55600 number of atom coordinates read : 2081 total number of charged atoms : 1947 net assigned charge : 5.945010 assigned positive charge : 317.6060 centred at (gu) : 87.73250 87.71711 92.57426 assigned negative charge : -311.6611 centred at (gu) : 87.26598 87.80026 92.76128 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77312 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17430 grid for indexing accessible points = 1.400000 m= 31752 mr = 55114 m= 6420 mr = 24258 m= 585 mr = 4352 m= 12 mr = 294 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 32063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 15479 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) : 0.7198318 object centre at (A) : 2.892001 7.656001 21.55600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2898010E-02 6.2661707E-02 midg,1,midg; midg,igrid,midg 3.8225338E-02 2.8499030E-03 1,midg,midg; igrid,midg,midg 1.0551332E-02 3.7541986E-02 gauss-seidel spectral radius is 0.9988645 estimated iterations to convergence 235 setup time was (sec) 0.8300000 now iterating at: 08:32:49 rms-change max change #iterations 4.785558 196.3749 at 10iterations 2.390172 84.50545 at 20iterations 1.198961 41.16582 at 30iterations 0.5998685 18.42755 at 40iterations 0.3021128 9.876174 at 50iterations 0.1512722 4.404369 at 60iterations 7.6201163E-02 2.309380 at 70iterations 3.8314857E-02 1.088549 at 80iterations 1.9261256E-02 0.6025734 at 90iterations 9.7071901E-03 0.3328848 at 100iterations 4.9078702E-03 0.1496153 at 110iterations 2.5189596E-03 7.5592041E-02 at 120iterations finished qdiffx linear iterations at : 08:32:55 total time elapsed so far: 6.700000 # loops : 120 mean,max change (kT/e) : 2.5189596E-03 7.5592041E-02 energy calculations done at 6.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.930000 DelPhi exited at 08:32:56 6.932u 0.167s 0:07.56 93.7% 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 08:32:56 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2081 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: GLM 174 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.239243 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): -20.75200 26.53600 ymin,ymax (A): -10.84000 26.15200 zmin,zma (A): -3.172000 46.28400 x,y,z range (A): 47.28800 36.99200 49.45600 scale (grids/A): 3.239243 object centre (A): 2.892001 7.656001 21.55600 number of atom coordinates read : 2081 total number of charged atoms : 1947 net assigned charge : 5.945010 assigned positive charge : 317.6060 centred at (gu) : 86.59872 86.57565 93.86146 assigned negative charge : -311.6611 centred at (gu) : 85.89893 86.70036 94.14198 start vw surface at 0.1200000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 178093 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17430 grid for indexing accessible points = 1.400000 m= 97735 mr = 132268 m= 40932 mr = 81836 m= 12084 mr = 33805 m= 2441 mr = 9424 m= 296 mr = 1786 m= 10 mr = 188 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.800000 number of dielectric boundary points 72284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 15576 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) : 2.159495 object centre at (A) : 2.892001 7.656001 21.55600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3029856 0.7308426 midg,1,midg; midg,igrid,midg 0.3141489 -1.5578623E-02 1,midg,midg; igrid,midg,midg 0.3559179 0.3377186 gauss-seidel spectral radius is 0.9993034 estimated iterations to convergence 299 setup time was (sec) 2.080000 now iterating at: 08:32:58 rms-change max change #iterations 10.61090 401.1606 at 10iterations 6.321249 125.5939 at 20iterations 3.752312 81.88376 at 30iterations 2.220896 40.93801 at 40iterations 1.310832 23.73392 at 50iterations 0.7743095 13.34278 at 60iterations 0.4557203 8.943525 at 70iterations 0.2687006 4.667175 at 80iterations 0.1577555 2.630205 at 90iterations 9.3003795E-02 1.563175 at 100iterations 5.4738101E-02 0.9014816 at 110iterations 3.2320648E-02 0.5980787 at 120iterations 1.9237245E-02 0.3277664 at 130iterations 1.1602430E-02 0.2018318 at 140iterations 7.1611507E-03 0.1375139 at 150iterations 4.5866589E-03 8.4518433E-02 at 160iterations 3.0857900E-03 5.6373596E-02 at 170iterations 2.1997120E-03 3.6991119E-02 at 180iterations finished qdiffx linear iterations at : 08:33:07 total time elapsed so far: 11.34000 # loops : 180 mean,max change (kT/e) : 2.1997120E-03 3.6991119E-02 energy calculations done at 11.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.54000 DelPhi exited at 08:33:08 11.540u 0.186s 0:12.15 96.4% 0+0k 0+0io 0pf+0w