Sat Oct 8 19:04:53 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+sph.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 = amb.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 19:04:53 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6261983 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): -32.08400 17.40400 ymin,ymax (A): -24.03000 22.79100 zmin,zma (A): -12.80600 44.04500 x,y,z range (A): 49.48800 46.82100 56.85100 scale (grids/A): 0.6261983 object centre (A): -7.340000 -0.6194992 15.61950 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.54778 89.12763 90.23313 assigned negative charge : -388.8955 centred at (gu) : 88.44185 89.16180 90.12257 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6839 nv = 96 ne = 84 npr = 53213 no. pairs analyzed = 53213 no. exposed pairs = 3082 no. arc points = 22023 no. surface atoms = 1040 nbur = 1566 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3839 m= 4 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 72 time to turn everything in is 0.3700000 number of dielectric boundary points 3297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2212 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8263 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1907007E-09 1.3807506E-08 midg,1,midg; midg,igrid,midg 8.6446610E-09 1.4661051E-09 1,midg,midg; igrid,midg,midg -5.7182343E-09 9.3186374E-09 gauss-seidel spectral radius is 0.9867919 estimated iterations to convergence 71 setup time was (sec) 0.7000000 now iterating at: 19:04:54 rms-change max change #iterations 0.1353682 24.02215 at 10iterations 1.2826346E-02 2.159798 at 20iterations 1.2288333E-03 0.1893311 at 30iterations 1.1431463E-04 1.9447327E-02 at 40iterations 1.0805691E-05 1.5716553E-03 at 50iterations finished qdiffx linear iterations at : 19:04:57 total time elapsed so far: 4.200000 # loops : 50 mean,max change (kT/e) : 1.0805691E-05 1.5716553E-03 energy calculations done at 4.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.390000 DelPhi exited at 19:04:58 4.392u 0.275s 0:04.95 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 Sat Oct 8 2011 at 19:04:58 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.878595 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): -32.08400 17.40400 ymin,ymax (A): -24.03000 22.79100 zmin,zma (A): -12.80600 44.04500 x,y,z range (A): 49.48800 46.82100 56.85100 scale (grids/A): 1.878595 object centre (A): -7.340000 -0.6194992 15.61950 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 85.64302 87.38245 90.69871 assigned negative charge : -388.8955 centred at (gu) : 85.32522 87.48522 90.36759 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73821 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22023 grid for indexing accessible points = 1.400000 m= 28004 mr = 51828 m= 4520 mr = 21144 m= 229 mr = 3042 m= 4 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1890 time to turn everything in is 0.5700000 number of dielectric boundary points 30484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19386 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) : 0.6261983 object centre at (A) : -7.340000 -0.6194992 15.61950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4367487E-02 3.2924324E-02 midg,1,midg; midg,igrid,midg 1.1690300E-02 1.4432559E-03 1,midg,midg; igrid,midg,midg -2.3910452E-03 3.8290769E-02 gauss-seidel spectral radius is 0.9985999 estimated iterations to convergence 212 setup time was (sec) 0.8900000 now iterating at: 19:04:59 rms-change max change #iterations 4.099952 162.3199 at 10iterations 1.906303 63.81631 at 20iterations 0.8841099 30.51195 at 30iterations 0.4084872 16.20400 at 40iterations 0.1900868 5.980129 at 50iterations 8.8429406E-02 2.993866 at 60iterations 4.1077126E-02 1.467364 at 70iterations 1.8952522E-02 0.5842056 at 80iterations 8.7765586E-03 0.2804985 at 90iterations 4.0931255E-03 0.1356392 at 100iterations 1.8935049E-03 6.0631752E-02 at 110iterations 8.8326033E-04 2.7542114E-02 at 120iterations finished qdiffx linear iterations at : 19:05:07 total time elapsed so far: 9.230000 # loops : 120 mean,max change (kT/e) : 8.8326033E-04 2.7542114E-02 energy calculations done at 9.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.420000 DelPhi exited at 19:05:08 9.419u 0.252s 0:09.93 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 19:05:08 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.817892 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): -32.08400 17.40400 ymin,ymax (A): -24.03000 22.79100 zmin,zma (A): -12.80600 44.04500 x,y,z range (A): 49.48800 46.82100 56.85100 scale (grids/A): 2.817892 object centre (A): -7.340000 -0.6194992 15.61950 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 83.46442 86.07349 91.04790 assigned negative charge : -388.8955 centred at (gu) : 82.98783 86.22784 90.55132 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 170527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22023 grid for indexing accessible points = 1.400000 m= 88922 mr = 124778 m= 33383 mr = 74044 m= 8259 mr = 27395 m= 1196 mr = 6493 m= 46 mr = 828 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 6292 time to turn everything in is 1.430000 number of dielectric boundary points 68773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 19727 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) : 1.878595 object centre at (A) : -7.340000 -0.6194992 15.61950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4045283E-02 0.4794087 midg,1,midg; midg,igrid,midg 0.1421285 1.4572228E-02 1,midg,midg; igrid,midg,midg -1.6278939E-02 0.4669974 gauss-seidel spectral radius is 0.9992439 estimated iterations to convergence 287 setup time was (sec) 1.760000 now iterating at: 19:05:10 rms-change max change #iterations 9.658231 471.4011 at 10iterations 5.553855 110.2637 at 20iterations 3.175997 64.55125 at 30iterations 1.818817 33.71238 at 40iterations 1.038645 19.70022 at 50iterations 0.5928385 12.92625 at 60iterations 0.3384835 6.253160 at 70iterations 0.1937461 3.483862 at 80iterations 0.1106657 1.935186 at 90iterations 6.2948808E-02 1.130920 at 100iterations 3.6076996E-02 0.6589918 at 110iterations 2.0512892E-02 0.4125328 at 120iterations 1.1725026E-02 0.2059584 at 130iterations 6.6893357E-03 0.1221790 at 140iterations 3.8091065E-03 7.0030212E-02 at 150iterations 2.1786143E-03 4.4244766E-02 at 160iterations 1.2427801E-03 2.2629738E-02 at 170iterations 7.0942141E-04 1.2477875E-02 at 180iterations finished qdiffx linear iterations at : 19:05:23 total time elapsed so far: 14.86000 # loops : 180 mean,max change (kT/e) : 7.0942141E-04 1.2477875E-02 energy calculations done at 14.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.04000 DelPhi exited at 19:05:23 15.044u 0.274s 0:15.58 98.2% 0+0k 0+0io 0pf+0w