Sat Oct 15 14:18:29 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 15 2011 at 14:18:29 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4807 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5133307 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): -18.28900 37.35700 ymin,ymax (A): -30.85800 35.53000 zmin,zma (A): -4.175000 65.17600 x,y,z range (A): 55.64600 66.38800 69.35101 scale (grids/A): 0.5133307 object centre (A): 9.534001 2.336001 30.50050 number of atom coordinates read : 4807 total number of charged atoms : 4560 net assigned charge : 5.800031 assigned positive charge : 722.4222 centred at (gu) : 90.03751 90.20908 88.44233 assigned negative charge : -716.6270 centred at (gu) : 89.93408 90.25780 88.45087 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8010 nv = 96 ne = 84 npr = 97150 no. pairs analyzed = 97150 no. exposed pairs = 6154 no. arc points = 42408 no. surface atoms = 2063 nbur = 2744 mkacc time = 0.2100000 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 = 1.652000 m= 277 mr = 4102 m= 0 mr = 7 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4121 ## 600 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10672 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7599337E-10 4.5978183E-11 midg,1,midg; midg,igrid,midg 2.2130903E-10 -5.3515921E-11 1,midg,midg; igrid,midg,midg -2.1106282E-10 3.9398440E-10 gauss-seidel spectral radius is 0.9805959 estimated iterations to convergence 59 setup time was (sec) 0.6500000 now iterating at: 14:18:30 rms-change max change #iterations 7.0633255E-02 9.438476 at 10iterations 5.0969399E-03 0.9654045 at 20iterations 9.9740806E-04 0.1573715 at 30iterations 3.5768512E-04 4.2869568E-02 at 40iterations 1.4483233E-04 1.9740209E-02 at 50iterations finished qdiffx linear iterations at : 14:18:32 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 1.4483233E-04 1.9740209E-02 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 14:18:33 3.289u 0.166s 0:03.75 91.7% 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 14:18:33 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4807 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.539992 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): -18.28900 37.35700 ymin,ymax (A): -30.85800 35.53000 zmin,zma (A): -4.175000 65.17600 x,y,z range (A): 55.64600 66.38800 69.35101 scale (grids/A): 1.539992 object centre (A): 9.534001 2.336001 30.50050 number of atom coordinates read : 4807 total number of charged atoms : 4560 net assigned charge : 5.800031 assigned positive charge : 722.4222 centred at (gu) : 90.11105 90.62567 85.32517 assigned negative charge : -716.6270 centred at (gu) : 89.80203 90.77313 85.35242 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 91089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42408 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26387 mr = 62533 m= 2265 mr = 17278 m= 47 mr = 922 m= 1 mr = 4 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 39053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 489 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 34313 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) : 0.5133307 object centre at (A) : 9.534001 2.336001 30.50050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5571871E-03 1.6923089E-02 midg,1,midg; midg,igrid,midg 6.4950944E-03 -1.1634069E-02 1,midg,midg; igrid,midg,midg -5.7663250E-04 1.2335725E-02 gauss-seidel spectral radius is 0.9981416 estimated iterations to convergence 184 setup time was (sec) 0.9000000 now iterating at: 14:18:34 rms-change max change #iterations 3.845318 142.2562 at 10iterations 1.585444 49.98377 at 20iterations 0.6556247 20.64718 at 30iterations 0.2706920 8.381852 at 40iterations 0.1123316 3.637959 at 50iterations 4.6716612E-02 1.558616 at 60iterations 1.9415967E-02 0.6107855 at 70iterations 8.1577534E-03 0.2651215 at 80iterations 3.5218692E-03 0.1102016 at 90iterations 1.6180817E-03 6.0296938E-02 at 100iterations 8.3510991E-04 2.5835037E-02 at 110iterations 5.0158700E-04 1.4863610E-02 at 120iterations finished qdiffx linear iterations at : 14:18:40 total time elapsed so far: 7.010000 # loops : 120 mean,max change (kT/e) : 5.0158700E-04 1.4863610E-02 energy calculations done at 7.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.170000 DelPhi exited at 14:18:41 7.177u 0.184s 0:07.79 94.3% 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 14:18:41 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4807 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.309988 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): -18.28900 37.35700 ymin,ymax (A): -30.85800 35.53000 zmin,zma (A): -4.175000 65.17600 x,y,z range (A): 55.64600 66.38800 69.35101 scale (grids/A): 2.309988 object centre (A): 9.534001 2.336001 30.50050 number of atom coordinates read : 4807 total number of charged atoms : 4560 net assigned charge : 5.800031 assigned positive charge : 722.4222 centred at (gu) : 90.16616 90.93797 82.98754 assigned negative charge : -716.6270 centred at (gu) : 89.70316 91.15966 83.02867 start vw surface at 0.1900000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 212310 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42408 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 95313 mr = 153702 m= 23515 mr = 74217 m= 3253 mr = 16420 m= 196 mr = 1925 m= 1 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.480000 number of dielectric boundary points 88256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 36395 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) : 1.539992 object centre at (A) : 9.534001 2.336001 30.50050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1764578 0.4591134 midg,1,midg; midg,igrid,midg 6.8311967E-02 -0.2849815 1,midg,midg; igrid,midg,midg -2.9589918E-03 0.1840186 gauss-seidel spectral radius is 0.9991743 estimated iterations to convergence 275 setup time was (sec) 1.780000 now iterating at: 14:18:43 rms-change max change #iterations 10.45921 292.0465 at 10iterations 6.029348 164.9883 at 20iterations 3.464188 80.06647 at 30iterations 1.964001 45.85473 at 40iterations 1.114107 24.68854 at 50iterations 0.6284110 13.74253 at 60iterations 0.3535430 8.092372 at 70iterations 0.1989345 4.223221 at 80iterations 0.1117027 2.131420 at 90iterations 6.2690862E-02 1.452606 at 100iterations 3.5067745E-02 0.7126241 at 110iterations 1.9603467E-02 0.3741565 at 120iterations 1.0967761E-02 0.2197137 at 130iterations 6.1340472E-03 0.1196022 at 140iterations 3.4325623E-03 6.7207336E-02 at 150iterations 1.9271403E-03 3.6351681E-02 at 160iterations 1.0866787E-03 2.0154715E-02 at 170iterations 6.1792892E-04 1.1379242E-02 at 180iterations finished qdiffx linear iterations at : 14:18:52 total time elapsed so far: 11.62000 # loops : 180 mean,max change (kT/e) : 6.1792892E-04 1.1379242E-02 energy calculations done at 11.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.80000 DelPhi exited at 14:18:53 11.800u 0.178s 0:12.53 95.5% 0+0k 0+0io 0pf+0w