Mon Oct 10 14:02:26 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 Mon Oct 10 2011 at 14:02:27 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 !!! WARNING: CME 114 has a net charge of -0.3480 !!! WARNING: HIR 214 has a net charge of 0.5140 !!! WARNING: CME 220 has a net charge of -0.3480 !!! WARNING: CME 316 has a net charge of -0.3480 !!! WARNING: CME 465 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of 0.1000 !!! WARNING: CME 6 has a net charge of -0.0350 !!! WARNING: CME 8 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5857768 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): -49.99700 10.77700 ymin,ymax (A): -25.35000 29.49300 zmin,zma (A): -27.94800 26.90800 x,y,z range (A): 60.77400 54.84300 54.85600 scale (grids/A): 0.5857768 object centre (A): -19.61000 2.071500 -0.5200005 number of atom coordinates read : 3001 total number of charged atoms : 2898 net assigned charge : 2.082026 assigned positive charge : 447.7068 centred at (gu) : 89.59913 89.92603 91.10108 assigned negative charge : -445.6267 centred at (gu) : 89.56496 89.85797 91.03960 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7087 nv = 96 ne = 84 npr = 58481 no. pairs analyzed = 58481 no. exposed pairs = 4117 no. arc points = 28804 no. surface atoms = 1369 nbur = 1632 mkacc time = 0.1000000 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 = 1.484000 m= 355 mr = 3594 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2100000 number of dielectric boundary points 3824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2860 ## 290 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8863 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5153790E-10 2.8077463E-09 midg,1,midg; midg,igrid,midg -1.3114700E-09 2.3007165E-09 1,midg,midg; igrid,midg,midg -4.1376311E-10 1.3197536E-09 gauss-seidel spectral radius is 0.9849714 estimated iterations to convergence 67 setup time was (sec) 0.4000000 now iterating at: 14:02:27 rms-change max change #iterations 0.1024725 17.44470 at 10iterations 8.6256629E-03 1.283188 at 20iterations 8.6578896E-04 0.1220093 at 30iterations 1.4972290E-04 2.3241043E-02 at 40iterations 3.6225058E-05 5.2967072E-03 at 50iterations finished qdiffx linear iterations at : 14:02:30 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.6225058E-05 5.2967072E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 14:02:31 3.419u 0.180s 0:04.33 82.9% 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 Mon Oct 10 2011 at 14:02:31 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 !!! WARNING: CME 114 has a net charge of -0.3480 !!! WARNING: HIR 214 has a net charge of 0.5140 !!! WARNING: CME 220 has a net charge of -0.3480 !!! WARNING: CME 316 has a net charge of -0.3480 !!! WARNING: CME 465 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of 0.1000 !!! WARNING: CME 6 has a net charge of -0.0350 !!! WARNING: CME 8 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.757331 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): -49.99700 10.77700 ymin,ymax (A): -25.35000 29.49300 zmin,zma (A): -27.94800 26.90800 x,y,z range (A): 60.77400 54.84300 54.85600 scale (grids/A): 1.757331 object centre (A): -19.61000 2.071500 -0.5200005 number of atom coordinates read : 3001 total number of charged atoms : 2898 net assigned charge : 2.082026 assigned positive charge : 447.7068 centred at (gu) : 88.79663 89.77716 93.30241 assigned negative charge : -445.6267 centred at (gu) : 88.69486 89.57371 93.11884 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77425 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28804 grid for indexing accessible points = 1.400000 m= 25929 mr = 51853 m= 3691 mr = 17676 m= 146 mr = 1977 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 496 time to turn everything in is 0.3800000 number of dielectric boundary points 35654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 238 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 22591 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) : 0.5857768 object centre at (A) : -19.61000 2.071500 -0.5200005 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5013468E-03 1.2951148E-02 midg,1,midg; midg,igrid,midg 2.3957854E-03 1.6204467E-02 1,midg,midg; igrid,midg,midg -2.4260773E-04 -6.7393025E-03 gauss-seidel spectral radius is 0.9984674 estimated iterations to convergence 203 setup time was (sec) 0.5900000 now iterating at: 14:02:32 rms-change max change #iterations 3.922824 189.9060 at 10iterations 1.746392 66.38354 at 20iterations 0.7801989 26.14700 at 30iterations 0.3482487 11.84662 at 40iterations 0.1557059 5.813636 at 50iterations 6.9682449E-02 2.245590 at 60iterations 3.1207757E-02 0.9510040 at 70iterations 1.3972461E-02 0.4675756 at 80iterations 6.3002626E-03 0.2068396 at 90iterations 2.8424077E-03 9.5714569E-02 at 100iterations 1.2921937E-03 4.0208817E-02 at 110iterations 5.9561152E-04 1.9920349E-02 at 120iterations finished qdiffx linear iterations at : 14:02:39 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 5.9561152E-04 1.9920349E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 14:02:40 7.853u 0.209s 0:08.55 94.1% 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 Mon Oct 10 2011 at 14:02:40 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3001 !!! WARNING: CME 114 has a net charge of -0.3480 !!! WARNING: HIR 214 has a net charge of 0.5140 !!! WARNING: CME 220 has a net charge of -0.3480 !!! WARNING: CME 316 has a net charge of -0.3480 !!! WARNING: CME 465 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of 0.1000 !!! WARNING: CME 6 has a net charge of -0.0350 !!! WARNING: CME 8 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.635996 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): -49.99700 10.77700 ymin,ymax (A): -25.35000 29.49300 zmin,zma (A): -27.94800 26.90800 x,y,z range (A): 60.77400 54.84300 54.85600 scale (grids/A): 2.635996 object centre (A): -19.61000 2.071500 -0.5200005 number of atom coordinates read : 3001 total number of charged atoms : 2898 net assigned charge : 2.082026 assigned positive charge : 447.7068 centred at (gu) : 88.19473 89.66549 94.95346 assigned negative charge : -445.6267 centred at (gu) : 88.04229 89.36044 94.67818 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 179538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28804 grid for indexing accessible points = 1.400000 m= 85703 mr = 127276 m= 28654 mr = 66864 m= 6329 mr = 21582 m= 648 mr = 4345 m= 14 mr = 342 m= 0 mr = 6 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 1446 time to turn everything in is 0.9700000 number of dielectric boundary points 80471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 23176 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) : 1.757331 object centre at (A) : -19.61000 2.071500 -0.5200005 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8809364E-02 0.1786905 midg,1,midg; midg,igrid,midg 0.1427014 0.1987235 1,midg,midg; igrid,midg,midg 1.8159987E-02 -0.1819838 gauss-seidel spectral radius is 0.9992312 estimated iterations to convergence 285 setup time was (sec) 1.210000 now iterating at: 14:02:41 rms-change max change #iterations 9.827142 274.6374 at 10iterations 5.781449 160.0911 at 20iterations 3.367925 87.34366 at 30iterations 1.950908 37.08460 at 40iterations 1.127749 22.37633 at 50iterations 0.6485571 13.36727 at 60iterations 0.3715394 7.231325 at 70iterations 0.2134900 4.059469 at 80iterations 0.1217588 2.251938 at 90iterations 6.9590382E-02 1.317215 at 100iterations 3.9691892E-02 0.8222580 at 110iterations 2.2641070E-02 0.4089447 at 120iterations 1.2941314E-02 0.2298212 at 130iterations 7.3843529E-03 0.1340168 at 140iterations 4.2145024E-03 9.1573715E-02 at 150iterations 2.4138223E-03 4.5450211E-02 at 160iterations 1.3868778E-03 2.5249481E-02 at 170iterations 8.0361735E-04 1.7923355E-02 at 180iterations finished qdiffx linear iterations at : 14:02:53 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 8.0361735E-04 1.7923355E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 14:02:54 12.787u 0.198s 0:13.69 94.7% 0+0k 0+0io 0pf+0w