Tue Oct 11 06:59:06 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 06:59:06 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3048 !!! WARNING: UMP 317 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5664370 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): -17.85500 44.99400 ymin,ymax (A): 19.20200 77.35900 zmin,zma (A): -69.94100 -19.73200 x,y,z range (A): 62.84900 58.15700 50.20900 scale (grids/A): 0.5664370 object centre (A): 13.56950 48.28050 -44.83650 number of atom coordinates read : 3048 total number of charged atoms : 2904 net assigned charge : -5.099982 assigned positive charge : 444.7764 centred at (gu) : 89.62948 89.96472 89.65884 assigned negative charge : -449.8770 centred at (gu) : 89.61439 90.16986 89.62940 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6451 nv = 96 ne = 84 npr = 63161 no. pairs analyzed = 63161 no. exposed pairs = 3843 no. arc points = 26792 no. surface atoms = 1308 nbur = 1740 mkacc time = 0.1300000 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 = 1.512000 m= 299 mr = 3403 m= 0 mr = 9 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2662 ## 275 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8225 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1913968E-09 -2.5155616E-10 midg,1,midg; midg,igrid,midg 2.1505486E-09 -3.6117469E-09 1,midg,midg; igrid,midg,midg -9.7750408E-10 -4.3347276E-10 gauss-seidel spectral radius is 0.9839282 estimated iterations to convergence 65 setup time was (sec) 0.5500000 now iterating at: 06:59:07 rms-change max change #iterations 8.7807089E-02 16.82235 at 10iterations 6.4993710E-03 0.9488897 at 20iterations 4.7385105E-04 7.8897476E-02 at 30iterations 3.5229426E-05 5.5923462E-03 at 40iterations 2.7096014E-06 4.2152405E-04 at 50iterations finished qdiffx linear iterations at : 06:59:09 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 2.7096014E-06 4.2152405E-04 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 06:59:10 3.149u 0.140s 0:04.10 80.0% 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 06:59:10 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3048 !!! WARNING: UMP 317 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.699311 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): -17.85500 44.99400 ymin,ymax (A): 19.20200 77.35900 zmin,zma (A): -69.94100 -19.73200 x,y,z range (A): 62.84900 58.15700 50.20900 scale (grids/A): 1.699311 object centre (A): 13.56950 48.28050 -44.83650 number of atom coordinates read : 3048 total number of charged atoms : 2904 net assigned charge : -5.099982 assigned positive charge : 444.7764 centred at (gu) : 88.88777 89.89317 88.97575 assigned negative charge : -449.8770 centred at (gu) : 88.84277 90.50906 88.88782 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26792 grid for indexing accessible points = 1.400000 m= 23407 mr = 47826 m= 2658 mr = 16576 m= 68 mr = 1337 m= 0 mr = 9 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 503 time to turn everything in is 0.5000000 number of dielectric boundary points 30784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 220 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 22433 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) : 0.5664370 object centre at (A) : 13.56950 48.28050 -44.83650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9106490E-03 1.6201414E-02 midg,1,midg; midg,igrid,midg -9.7920815E-04 -2.3765558E-02 1,midg,midg; igrid,midg,midg -1.4039494E-02 -2.4609819E-02 gauss-seidel spectral radius is 0.9983408 estimated iterations to convergence 195 setup time was (sec) 0.7700000 now iterating at: 06:59:11 rms-change max change #iterations 3.624408 173.7804 at 10iterations 1.564044 56.23521 at 20iterations 0.6742626 26.04263 at 30iterations 0.2933434 9.958145 at 40iterations 0.1268021 4.532701 at 50iterations 5.5077523E-02 1.886834 at 60iterations 2.3899663E-02 0.7682753 at 70iterations 1.0303134E-02 0.4050751 at 80iterations 4.4632289E-03 0.1458434 at 90iterations 1.9343293E-03 6.3372612E-02 at 100iterations 8.4156939E-04 2.9047966E-02 at 110iterations 3.6491780E-04 1.2669563E-02 at 120iterations finished qdiffx linear iterations at : 06:59:17 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 3.6491780E-04 1.2669563E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 06:59:18 6.922u 0.153s 0:07.40 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 06:59:18 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3048 !!! WARNING: UMP 317 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.548966 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): -17.85500 44.99400 ymin,ymax (A): 19.20200 77.35900 zmin,zma (A): -69.94100 -19.73200 x,y,z range (A): 62.84900 58.15700 50.20900 scale (grids/A): 2.548966 object centre (A): 13.56950 48.28050 -44.83650 number of atom coordinates read : 3048 total number of charged atoms : 2904 net assigned charge : -5.099982 assigned positive charge : 444.7764 centred at (gu) : 88.33162 89.83977 88.46363 assigned negative charge : -449.8770 centred at (gu) : 88.26410 90.76353 88.33152 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 162948 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26792 grid for indexing accessible points = 1.400000 m= 78657 mr = 116647 m= 24564 mr = 62946 m= 4433 mr = 18790 m= 361 mr = 2942 m= 9 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 1553 time to turn everything in is 1.150000 number of dielectric boundary points 69492 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 23221 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) : 1.699311 object centre at (A) : 13.56950 48.28050 -44.83650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1116612 0.3009674 midg,1,midg; midg,igrid,midg -1.5657863E-02 -0.2147756 1,midg,midg; igrid,midg,midg -0.2033050 -0.3298692 gauss-seidel spectral radius is 0.9991888 estimated iterations to convergence 277 setup time was (sec) 1.440000 now iterating at: 06:59:19 rms-change max change #iterations 9.184822 277.0889 at 10iterations 5.254752 117.6824 at 20iterations 2.970895 60.80529 at 30iterations 1.679690 35.51257 at 40iterations 0.9457314 19.44058 at 50iterations 0.5321215 12.92210 at 60iterations 0.2992448 6.075095 at 70iterations 0.1675350 3.245375 at 80iterations 9.3932934E-02 1.748228 at 90iterations 5.2562866E-02 1.188365 at 100iterations 2.9376211E-02 0.5321198 at 110iterations 1.6440568E-02 0.3464689 at 120iterations 9.1914237E-03 0.1946106 at 130iterations 5.1411442E-03 0.1013355 at 140iterations 2.8727152E-03 5.6083679E-02 at 150iterations 1.6074053E-03 2.9010773E-02 at 160iterations 8.9916546E-04 1.7669678E-02 at 170iterations 5.0247647E-04 1.0101318E-02 at 180iterations finished qdiffx linear iterations at : 06:59:29 total time elapsed so far: 10.77000 # loops : 180 mean,max change (kT/e) : 5.0247647E-04 1.0101318E-02 energy calculations done at 10.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.95000 DelPhi exited at 06:59:30 10.951u 0.174s 0:11.93 93.2% 0+0k 0+0io 0pf+0w