Sat Oct 8 21:39:42 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 Sat Oct 8 2011 at 21:39:42 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2025 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: GLM 133 has a net charge of -0.0940 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: 0.6656072 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): 6.253000 59.73800 ymin,ymax (A): 2.846000 50.09300 zmin,zma (A): 12.74300 55.90200 x,y,z range (A): 53.48500 47.24700 43.15900 scale (grids/A): 0.6656072 object centre (A): 32.99550 26.46950 34.32250 number of atom coordinates read : 2025 total number of charged atoms : 1885 net assigned charge : -7.9996467E-02 assigned positive charge : 302.6428 centred at (gu) : 87.83532 89.37947 89.60798 assigned negative charge : -302.7228 centred at (gu) : 87.95473 89.42619 89.64730 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6049 nv = 96 ne = 84 npr = 40807 no. pairs analyzed = 40807 no. exposed pairs = 2554 no. arc points = 18238 no. surface atoms = 869 nbur = 1156 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 373 mr = 3302 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1678 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6443411E-09 -7.1959732E-09 midg,1,midg; midg,igrid,midg 8.4551841E-09 -8.0197582E-09 1,midg,midg; igrid,midg,midg 3.1865245E-08 -1.4173859E-08 gauss-seidel spectral radius is 0.9882487 estimated iterations to convergence 75 setup time was (sec) 0.5000000 now iterating at: 21:39:43 rms-change max change #iterations 0.1494379 21.37539 at 10iterations 1.6066622E-02 2.603970 at 20iterations 1.7243335E-03 0.2616625 at 30iterations 1.9150828E-04 2.8223991E-02 at 40iterations 2.4876377E-05 3.8204193E-03 at 50iterations finished qdiffx linear iterations at : 21:39:45 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 2.4876377E-05 3.8204193E-03 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 21:39:46 3.295u 0.182s 0:03.95 87.8% 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 21:39:46 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2025 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: GLM 133 has a net charge of -0.0940 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: 1.996822 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): 6.253000 59.73800 ymin,ymax (A): 2.846000 50.09300 zmin,zma (A): 12.74300 55.90200 x,y,z range (A): 53.48500 47.24700 43.15900 scale (grids/A): 1.996822 object centre (A): 32.99550 26.46950 34.32250 number of atom coordinates read : 2025 total number of charged atoms : 1885 net assigned charge : -7.9996467E-02 assigned positive charge : 302.6428 centred at (gu) : 83.50591 88.13828 88.82372 assigned negative charge : -302.7228 centred at (gu) : 83.86419 88.27850 88.94182 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 65039 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18238 grid for indexing accessible points = 1.400000 m= 23630 mr = 44785 m= 4158 mr = 17132 m= 264 mr = 2592 m= 1 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 28505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 14922 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) : 0.6656072 object centre at (A) : 32.99550 26.46950 34.32250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0164633E-02 -2.9598125E-03 midg,1,midg; midg,igrid,midg 2.6857547E-02 1.8147770E-03 1,midg,midg; igrid,midg,midg -3.6939014E-02 -4.5507722E-02 gauss-seidel spectral radius is 0.9986949 estimated iterations to convergence 219 setup time was (sec) 0.8000000 now iterating at: 21:39:47 rms-change max change #iterations 4.048780 182.3291 at 10iterations 1.930862 67.44550 at 20iterations 0.9136878 29.71247 at 30iterations 0.4374301 16.61844 at 40iterations 0.2077018 6.954281 at 50iterations 9.9084981E-02 3.383255 at 60iterations 4.7204569E-02 1.626112 at 70iterations 2.2374343E-02 0.7230225 at 80iterations 1.0708019E-02 0.3603134 at 90iterations 5.1143705E-03 0.1625347 at 100iterations 2.4422174E-03 8.3994627E-02 at 110iterations 1.1673411E-03 3.7395954E-02 at 120iterations finished qdiffx linear iterations at : 21:39:54 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 1.1673411E-03 3.7395954E-02 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.450000 DelPhi exited at 21:39:54 7.454u 0.200s 0:07.97 95.9% 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 Sat Oct 8 2011 at 21:39:54 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2025 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: GLM 133 has a net charge of -0.0940 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: 2.995232 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): 6.253000 59.73800 ymin,ymax (A): 2.846000 50.09300 zmin,zma (A): 12.74300 55.90200 x,y,z range (A): 53.48500 47.24700 43.15900 scale (grids/A): 2.995232 object centre (A): 32.99550 26.46950 34.32250 number of atom coordinates read : 2025 total number of charged atoms : 1885 net assigned charge : -7.9996467E-02 assigned positive charge : 302.6428 centred at (gu) : 80.25883 87.20746 88.23551 assigned negative charge : -302.7228 centred at (gu) : 80.79626 87.41775 88.41264 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 150295 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18238 grid for indexing accessible points = 1.400000 m= 75756 mr = 108242 m= 28474 mr = 61707 m= 7475 mr = 22714 m= 1198 mr = 5606 m= 51 mr = 756 m= 0 mr = 5 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 64219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 15079 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) : 1.996822 object centre at (A) : 32.99550 26.46950 34.32250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1191849 -2.5695981E-02 midg,1,midg; midg,igrid,midg 0.2442698 -5.9710503E-02 1,midg,midg; igrid,midg,midg -0.5845441 -0.6855889 gauss-seidel spectral radius is 0.9992648 estimated iterations to convergence 291 setup time was (sec) 1.550000 now iterating at: 21:39:56 rms-change max change #iterations 9.418499 378.1387 at 10iterations 5.545275 125.9175 at 20iterations 3.238667 69.96164 at 30iterations 1.887564 41.16771 at 40iterations 1.098986 24.67699 at 50iterations 0.6374874 14.13352 at 60iterations 0.3700932 8.077821 at 70iterations 0.2146252 4.372473 at 80iterations 0.1238660 2.431423 at 90iterations 7.1595065E-02 1.535774 at 100iterations 4.1312695E-02 0.7650757 at 110iterations 2.3856843E-02 0.4470711 at 120iterations 1.3774250E-02 0.2691545 at 130iterations 7.9624886E-03 0.1498108 at 140iterations 4.5967414E-03 9.7337723E-02 at 150iterations 2.6606238E-03 4.9556732E-02 at 160iterations 1.5458947E-03 2.8884888E-02 at 170iterations 9.0146990E-04 1.8194199E-02 at 180iterations finished qdiffx linear iterations at : 21:40:06 total time elapsed so far: 11.85000 # loops : 180 mean,max change (kT/e) : 9.0146990E-04 1.8194199E-02 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.04000 DelPhi exited at 21:40:07 12.040u 0.219s 0:12.58 97.3% 0+0k 0+0io 0pf+0w