Tue Oct 11 04:25:31 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 Tue Oct 11 2011 at 04:25:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2697 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: 0.6583692 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): -11.20500 37.08800 ymin,ymax (A): -26.30500 22.31600 zmin,zma (A): -8.231999 45.84100 x,y,z range (A): 48.29300 48.62100 54.07300 scale (grids/A): 0.6583692 object centre (A): 12.94150 -1.994500 18.80450 number of atom coordinates read : 2697 total number of charged atoms : 2549 net assigned charge : 3.500024 assigned positive charge : 407.6976 centred at (gu) : 90.07614 90.39213 91.22287 assigned negative charge : -404.1984 centred at (gu) : 89.83340 90.22173 91.25738 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7828 nv = 96 ne = 84 npr = 55323 no. pairs analyzed = 55323 no. exposed pairs = 3280 no. arc points = 22843 no. surface atoms = 1110 nbur = 1587 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 436 mr = 4472 m= 5 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2100000 number of dielectric boundary points 3757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2165 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9229 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1901681E-08 2.0044486E-09 midg,1,midg; midg,igrid,midg -2.3648662E-08 4.5107953E-08 1,midg,midg; igrid,midg,midg -4.0004245E-08 5.6088268E-08 gauss-seidel spectral radius is 0.9880487 estimated iterations to convergence 75 setup time was (sec) 0.4100000 now iterating at: 04:25:31 rms-change max change #iterations 0.1688443 28.64502 at 10iterations 1.7844792E-02 2.640940 at 20iterations 1.9137244E-03 0.2401466 at 30iterations 2.0950718E-04 3.1036377E-02 at 40iterations 2.3863473E-05 3.3607483E-03 at 50iterations finished qdiffx linear iterations at : 04:25:34 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.3863473E-05 3.3607483E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 04:25:35 3.424u 0.168s 0:04.08 87.7% 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 04:25:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2697 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: 1.975108 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): -11.20500 37.08800 ymin,ymax (A): -26.30500 22.31600 zmin,zma (A): -8.231999 45.84100 x,y,z range (A): 48.29300 48.62100 54.07300 scale (grids/A): 1.975108 object centre (A): 12.94150 -1.994500 18.80450 number of atom coordinates read : 2697 total number of charged atoms : 2549 net assigned charge : 3.500024 assigned positive charge : 407.6976 centred at (gu) : 90.22803 91.17602 93.66795 assigned negative charge : -404.1984 centred at (gu) : 89.49989 90.66494 93.77161 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 84623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22843 grid for indexing accessible points = 1.400000 m= 31067 mr = 59982 m= 5003 mr = 23191 m= 275 mr = 3005 m= 3 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 211 time to turn everything in is 0.4200000 number of dielectric boundary points 34702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20120 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) : 0.6583692 object centre at (A) : 12.94150 -1.994500 18.80450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9147122E-02 -1.3299933E-02 midg,1,midg; midg,igrid,midg -1.2884759E-02 3.9415557E-02 1,midg,midg; igrid,midg,midg -1.3183836E-02 6.7296572E-02 gauss-seidel spectral radius is 0.9987372 estimated iterations to convergence 223 setup time was (sec) 0.6400000 now iterating at: 04:25:36 rms-change max change #iterations 4.631299 181.4964 at 10iterations 2.237671 73.29613 at 20iterations 1.080903 32.27253 at 30iterations 0.5190149 15.37225 at 40iterations 0.2524548 8.606552 at 50iterations 0.1219622 3.800356 at 60iterations 5.8470707E-02 1.755905 at 70iterations 2.8281666E-02 0.8050435 at 80iterations 1.3654173E-02 0.4361699 at 90iterations 6.6034221E-03 0.1877975 at 100iterations 3.1855688E-03 9.8531723E-02 at 110iterations 1.5365782E-03 4.4027328E-02 at 120iterations finished qdiffx linear iterations at : 04:25:43 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 1.5365782E-03 4.4027328E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 04:25:44 7.895u 0.201s 0:08.47 95.5% 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 04:25:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2697 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.962662 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): -11.20500 37.08800 ymin,ymax (A): -26.30500 22.31600 zmin,zma (A): -8.231999 45.84100 x,y,z range (A): 48.29300 48.62100 54.07300 scale (grids/A): 2.962662 object centre (A): 12.94150 -1.994500 18.80450 number of atom coordinates read : 2697 total number of charged atoms : 2549 net assigned charge : 3.500024 assigned positive charge : 407.6976 centred at (gu) : 90.34169 91.76379 95.50175 assigned negative charge : -404.1984 centred at (gu) : 89.24974 90.99730 95.65746 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 195379 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22843 grid for indexing accessible points = 1.400000 m= 100941 mr = 144694 m= 36649 mr = 83273 m= 8888 mr = 29499 m= 1333 mr = 6690 m= 69 mr = 825 m= 0 mr = 18 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 703 time to turn everything in is 1.070000 number of dielectric boundary points 78260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 20392 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) : 1.975108 object centre at (A) : 12.94150 -1.994500 18.80450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5959528 0.1092282 midg,1,midg; midg,igrid,midg -0.1476075 0.4663230 1,midg,midg; igrid,midg,midg -8.1464037E-02 0.5579409 gauss-seidel spectral radius is 0.9992813 estimated iterations to convergence 294 setup time was (sec) 1.320000 now iterating at: 04:25:45 rms-change max change #iterations 10.67785 399.2284 at 10iterations 6.255751 139.7415 at 20iterations 3.659897 68.13542 at 30iterations 2.134454 37.50992 at 40iterations 1.247270 25.25194 at 50iterations 0.7285275 13.97899 at 60iterations 0.4234343 7.467614 at 70iterations 0.2464981 4.191723 at 80iterations 0.1430203 2.420715 at 90iterations 8.3133519E-02 1.415012 at 100iterations 4.8400510E-02 0.8660507 at 110iterations 2.8127681E-02 0.4715176 at 120iterations 1.6325213E-02 0.2742691 at 130iterations 9.4784535E-03 0.1673732 at 140iterations 5.5075516E-03 9.8318100E-02 at 150iterations 3.2052537E-03 5.7945251E-02 at 160iterations 1.8641510E-03 3.2295227E-02 at 170iterations 1.0944955E-03 1.8316269E-02 at 180iterations finished qdiffx linear iterations at : 04:25:57 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 1.0944955E-03 1.8316269E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 04:25:57 12.886u 0.206s 0:13.39 97.6% 0+0k 0+0io 0pf+0w