Sat Oct 8 16:42:29 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 Sat Oct 8 2011 at 16:42:30 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4655 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 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: 0.5483166 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): 16.60900 78.83600 ymin,ymax (A): 118.3990 183.3250 zmin,zma (A): -5.274000 59.54600 x,y,z range (A): 62.22700 64.92599 64.82000 scale (grids/A): 0.5483166 object centre (A): 47.72250 150.8620 27.13600 number of atom coordinates read : 4655 total number of charged atoms : 4445 net assigned charge : 3.406045 assigned positive charge : 710.0787 centred at (gu) : 91.57922 89.20713 88.11020 assigned negative charge : -706.6759 centred at (gu) : 91.53881 89.11993 88.12336 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8887 nv = 96 ne = 84 npr = 95112 no. pairs analyzed = 95112 no. exposed pairs = 5433 no. arc points = 37941 no. surface atoms = 1833 nbur = 2822 mkacc time = 0.2600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 377 mr = 4869 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.5400000 number of dielectric boundary points 4361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3922 ## 529 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 11847 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0303745E-10 5.1744088E-11 midg,1,midg; midg,igrid,midg -9.5445263E-10 9.9795383E-10 1,midg,midg; igrid,midg,midg -1.5646397E-10 1.0195880E-09 gauss-seidel spectral radius is 0.9829714 estimated iterations to convergence 63 setup time was (sec) 0.8200000 now iterating at: 16:42:31 rms-change max change #iterations 9.7706921E-02 15.72638 at 10iterations 7.0157624E-03 0.9680462 at 20iterations 7.8024284E-04 0.1042576 at 30iterations 2.0879673E-04 2.8786659E-02 at 40iterations 6.8817310E-05 9.5167160E-03 at 50iterations finished qdiffx linear iterations at : 16:42:34 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 6.8817310E-05 9.5167160E-03 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.390000 DelPhi exited at 16:42:34 4.396u 0.297s 0:04.98 93.9% 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 Sat Oct 8 2011 at 16:42:35 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4655 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 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: 1.644950 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): 16.60900 78.83600 ymin,ymax (A): 118.3990 183.3250 zmin,zma (A): -5.274000 59.54600 x,y,z range (A): 62.22700 64.92599 64.82000 scale (grids/A): 1.644950 object centre (A): 47.72250 150.8620 27.13600 number of atom coordinates read : 4655 total number of charged atoms : 4445 net assigned charge : 3.406045 assigned positive charge : 710.0787 centred at (gu) : 94.73640 87.62019 84.32921 assigned negative charge : -706.6759 centred at (gu) : 94.61604 87.35948 84.36981 start vw surface at 0.2200000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 100120 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37941 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30984 mr = 70834 m= 3569 mr = 21643 m= 109 mr = 2053 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 1951 time to turn everything in is 0.8700000 number of dielectric boundary points 40243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 463 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 34098 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) : 0.5483166 object centre at (A) : 47.72250 150.8620 27.13600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6350105E-03 1.1754689E-02 midg,1,midg; midg,igrid,midg 1.5565698E-02 3.8277816E-02 1,midg,midg; igrid,midg,midg -1.1729170E-02 -1.5125074E-02 gauss-seidel spectral radius is 0.9983693 estimated iterations to convergence 197 setup time was (sec) 1.190000 now iterating at: 16:42:36 rms-change max change #iterations 4.436784 199.3408 at 10iterations 1.921725 96.85634 at 20iterations 0.8402131 28.28662 at 30iterations 0.3655650 13.40179 at 40iterations 0.1601358 4.742123 at 50iterations 7.0104949E-02 2.175751 at 60iterations 3.0662963E-02 0.9277025 at 70iterations 1.3459287E-02 0.3859253 at 80iterations 5.9004268E-03 0.1753006 at 90iterations 2.6005930E-03 7.2696686E-02 at 100iterations 1.1543815E-03 3.6933899E-02 at 110iterations 5.1952613E-04 1.5031815E-02 at 120iterations finished qdiffx linear iterations at : 16:42:45 total time elapsed so far: 10.03000 # loops : 120 mean,max change (kT/e) : 5.1952613E-04 1.5031815E-02 energy calculations done at 10.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.21000 DelPhi exited at 16:42:45 10.215u 0.315s 0:10.82 97.2% 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 Sat Oct 8 2011 at 16:42:45 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4655 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.467425 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): 16.60900 78.83600 ymin,ymax (A): 118.3990 183.3250 zmin,zma (A): -5.274000 59.54600 x,y,z range (A): 62.22700 64.92599 64.82000 scale (grids/A): 2.467425 object centre (A): 47.72250 150.8620 27.13600 number of atom coordinates read : 4655 total number of charged atoms : 4445 net assigned charge : 3.406045 assigned positive charge : 710.0787 centred at (gu) : 97.10444 86.42989 81.49358 assigned negative charge : -706.6759 centred at (gu) : 96.92395 86.03900 81.55463 start vw surface at 0.2200000 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 233198 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37941 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 107633 mr = 172817 m= 31254 mr = 86430 m= 5879 mr = 23795 m= 536 mr = 4251 m= 5 mr = 350 m= 0 mr = 0 time to grow re-entrant surface = 1.310000 no. cavity mid-points inaccessible to solvent = 6729 time to turn everything in is 2.190000 number of dielectric boundary points 90862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 2.350000 number of grid points assigned charge 35509 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) : 1.644950 object centre at (A) : 47.72250 150.8620 27.13600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3590268E-02 0.2628234 midg,1,midg; midg,igrid,midg 0.2348247 0.7165605 1,midg,midg; igrid,midg,midg -0.1757564 -0.2957704 gauss-seidel spectral radius is 0.9992231 estimated iterations to convergence 283 setup time was (sec) 2.540000 now iterating at: 16:42:48 rms-change max change #iterations 11.27340 406.4402 at 10iterations 6.520438 138.5414 at 20iterations 3.746203 73.26184 at 30iterations 2.151115 41.44060 at 40iterations 1.231407 22.76375 at 50iterations 0.7030672 12.14803 at 60iterations 0.4005272 7.419302 at 70iterations 0.2277267 4.025171 at 80iterations 0.1292924 2.262640 at 90iterations 7.3522821E-02 1.353956 at 100iterations 4.1733466E-02 0.6954975 at 110iterations 2.3697734E-02 0.3927193 at 120iterations 1.3462215E-02 0.2647815 at 130iterations 7.6236208E-03 0.1202564 at 140iterations 4.3292996E-03 7.6152802E-02 at 150iterations 2.4518075E-03 4.3603897E-02 at 160iterations 1.3921728E-03 2.2397995E-02 at 170iterations 7.9066708E-04 1.3065338E-02 at 180iterations finished qdiffx linear iterations at : 16:43:03 total time elapsed so far: 17.63000 # loops : 180 mean,max change (kT/e) : 7.9066708E-04 1.3065338E-02 energy calculations done at 17.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.82000 DelPhi exited at 16:43:04 17.817u 0.350s 0:18.51 98.1% 0+0k 0+0io 0pf+0w