Sat Oct 15 15:28:20 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 15 2011 at 15:28:21 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3452 !!! WARNING: HIR 193 has a net charge of 0.5140 !!! WARNING: SEP 349 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5523319 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): -65.09900 -18.48100 ymin,ymax (A): -48.86500 10.66900 zmin,zma (A): -54.78100 9.672999 x,y,z range (A): 46.61800 59.53400 64.45400 scale (grids/A): 0.5523319 object centre (A): -41.79000 -19.09800 -22.55400 number of atom coordinates read : 3452 total number of charged atoms : 3293 net assigned charge : -4.961008 assigned positive charge : 532.1487 centred at (gu) : 89.98923 89.67745 91.85261 assigned negative charge : -537.1108 centred at (gu) : 89.77296 89.32954 91.94445 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6811 nv = 96 ne = 84 npr = 68813 no. pairs analyzed = 68813 no. exposed pairs = 4418 no. arc points = 31184 no. surface atoms = 1463 nbur = 1989 mkacc time = 0.1200000 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 = 1.540000 m= 267 mr = 3501 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2500000 number of dielectric boundary points 3569 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3173 ## 416 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8942 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5347847E-10 -2.0442763E-09 midg,1,midg; midg,igrid,midg -4.3602602E-09 2.7829559E-09 1,midg,midg; igrid,midg,midg -2.6034694E-09 1.7715158E-09 gauss-seidel spectral radius is 0.9831319 estimated iterations to convergence 63 setup time was (sec) 0.4800000 now iterating at: 15:28:21 rms-change max change #iterations 8.8180684E-02 13.18917 at 10iterations 6.4736586E-03 1.081252 at 20iterations 7.2213332E-04 0.1031075 at 30iterations 1.5660252E-04 2.2830963E-02 at 40iterations 3.9904487E-05 5.6552887E-03 at 50iterations finished qdiffx linear iterations at : 15:28:25 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 3.9904487E-05 5.6552887E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 15:28:25 4.002u 0.248s 0:04.67 90.7% 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 Sat Oct 15 2011 at 15:28:25 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3452 !!! WARNING: HIR 193 has a net charge of 0.5140 !!! WARNING: SEP 349 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.656996 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): -65.09900 -18.48100 ymin,ymax (A): -48.86500 10.66900 zmin,zma (A): -54.78100 9.672999 x,y,z range (A): 46.61800 59.53400 64.45400 scale (grids/A): 1.656996 object centre (A): -41.79000 -19.09800 -22.55400 number of atom coordinates read : 3452 total number of charged atoms : 3293 net assigned charge : -4.961008 assigned positive charge : 532.1487 centred at (gu) : 89.96661 89.03162 95.55708 assigned negative charge : -537.1108 centred at (gu) : 89.31847 87.98824 95.83305 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 75562 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31184 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23889 mr = 51346 m= 2392 mr = 16317 m= 82 mr = 1112 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2457 time to turn everything in is 0.3900000 number of dielectric boundary points 33146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 376 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 25279 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) : 0.5523319 object centre at (A) : -41.79000 -19.09800 -22.55400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5531153E-02 -1.9664383E-02 midg,1,midg; midg,igrid,midg -5.3073302E-02 2.7252207E-02 1,midg,midg; igrid,midg,midg -9.6523389E-03 1.4455619E-02 gauss-seidel spectral radius is 0.9982919 estimated iterations to convergence 192 setup time was (sec) 0.6500000 now iterating at: 15:28:26 rms-change max change #iterations 3.852735 192.0471 at 10iterations 1.638384 62.41459 at 20iterations 0.6991242 24.19076 at 30iterations 0.3003480 9.994761 at 40iterations 0.1284035 4.331992 at 50iterations 5.5014044E-02 1.881058 at 60iterations 2.3607202E-02 0.8035202 at 70iterations 1.0149272E-02 0.3229284 at 80iterations 4.3819277E-03 0.1674271 at 90iterations 1.9093911E-03 6.4823382E-02 at 100iterations 8.4574509E-04 2.9209137E-02 at 110iterations 3.8598393E-04 1.3038635E-02 at 120iterations finished qdiffx linear iterations at : 15:28:35 total time elapsed so far: 9.040000 # loops : 120 mean,max change (kT/e) : 3.8598393E-04 1.3038635E-02 energy calculations done at 9.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.180000 DelPhi exited at 15:28:35 9.180u 0.296s 0:09.77 96.9% 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 15 2011 at 15:28:35 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3452 !!! WARNING: HIR 193 has a net charge of 0.5140 !!! WARNING: SEP 349 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.485493 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): -65.09900 -18.48100 ymin,ymax (A): -48.86500 10.66900 zmin,zma (A): -54.78100 9.672999 x,y,z range (A): 46.61800 59.53400 64.45400 scale (grids/A): 2.485493 object centre (A): -41.79000 -19.09800 -22.55400 number of atom coordinates read : 3452 total number of charged atoms : 3293 net assigned charge : -4.961008 assigned positive charge : 532.1487 centred at (gu) : 89.94952 88.54723 98.33553 assigned negative charge : -537.1108 centred at (gu) : 88.97761 86.98224 98.74941 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 175219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31184 grid for indexing accessible points = 1.400000 m= 82398 mr = 125374 m= 23442 mr = 65200 m= 3722 mr = 17344 m= 304 mr = 2254 m= 11 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 7912 time to turn everything in is 0.9800000 number of dielectric boundary points 74793 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 26325 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) : 1.656996 object centre at (A) : -41.79000 -19.09800 -22.55400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2066394 -0.2302622 midg,1,midg; midg,igrid,midg -0.7739918 0.3417202 1,midg,midg; igrid,midg,midg -6.4516790E-02 0.1868596 gauss-seidel spectral radius is 0.9991822 estimated iterations to convergence 276 setup time was (sec) 1.280000 now iterating at: 15:28:37 rms-change max change #iterations 9.823255 272.0302 at 10iterations 5.629273 138.3336 at 20iterations 3.190317 75.60137 at 30iterations 1.808318 41.99471 at 40iterations 1.020460 21.92025 at 50iterations 0.5757917 14.39683 at 60iterations 0.3233115 7.237936 at 70iterations 0.1815405 3.802290 at 80iterations 0.1020455 2.166851 at 90iterations 5.7234805E-02 1.059849 at 100iterations 3.2039661E-02 0.7268906 at 110iterations 1.7980361E-02 0.3727112 at 120iterations 1.0054362E-02 0.1960907 at 130iterations 5.6478553E-03 0.1108704 at 140iterations 3.1727783E-03 6.0073853E-02 at 150iterations 1.7888690E-03 3.8166046E-02 at 160iterations 1.0171222E-03 2.0428658E-02 at 170iterations 5.8430480E-04 1.0650635E-02 at 180iterations finished qdiffx linear iterations at : 15:28:50 total time elapsed so far: 15.08000 # loops : 180 mean,max change (kT/e) : 5.8430480E-04 1.0650635E-02 energy calculations done at 15.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.24000 DelPhi exited at 15:28:51 15.240u 0.314s 0:15.85 98.1% 0+0k 0+0io 0pf+0w