Sun Oct 9 11:39:27 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 Sun Oct 9 2011 at 11:39:27 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 !!! WARNING: ASP 359 has a net charge of -1.0260 !!! WARNING: HIR 475 has a net charge of 0.5140 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: 0.6255491 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): -0.9070000 56.00300 ymin,ymax (A): -19.48500 27.55200 zmin,zma (A): 93.57300 133.4380 x,y,z range (A): 56.91000 47.03700 39.86499 scale (grids/A): 0.6255491 object centre (A): 27.54800 4.033501 113.5055 number of atom coordinates read : 1956 total number of charged atoms : 1896 net assigned charge : 3.988007 assigned positive charge : 290.1879 centred at (gu) : 91.85193 90.74766 89.78347 assigned negative charge : -286.2004 centred at (gu) : 91.80630 90.67622 89.77580 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5451 nv = 96 ne = 84 npr = 37147 no. pairs analyzed = 37147 no. exposed pairs = 2670 no. arc points = 19468 no. surface atoms = 900 nbur = 1056 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 329 mr = 2770 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2953 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1973 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6530 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4078158E-09 3.9498680E-09 midg,1,midg; midg,igrid,midg -3.3415479E-10 9.1282812E-09 1,midg,midg; igrid,midg,midg 7.6568346E-10 9.4314601E-09 gauss-seidel spectral radius is 0.9867219 estimated iterations to convergence 71 setup time was (sec) 0.4800000 now iterating at: 11:39:28 rms-change max change #iterations 0.1140440 20.86504 at 10iterations 1.0565194E-02 2.164177 at 20iterations 9.8136242E-04 0.1420336 at 30iterations 9.1710572E-05 1.5851974E-02 at 40iterations 8.6338960E-06 1.4762878E-03 at 50iterations finished qdiffx linear iterations at : 11:39:31 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 8.6338960E-06 1.4762878E-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 11:39:31 3.293u 0.195s 0:03.77 92.3% 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 Sun Oct 9 2011 at 11:39:31 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 !!! WARNING: ASP 359 has a net charge of -1.0260 !!! WARNING: HIR 475 has a net charge of 0.5140 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: 1.876647 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): -0.9070000 56.00300 ymin,ymax (A): -19.48500 27.55200 zmin,zma (A): 93.57300 133.4380 x,y,z range (A): 56.91000 47.03700 39.86499 scale (grids/A): 1.876647 object centre (A): 27.54800 4.033501 113.5055 number of atom coordinates read : 1956 total number of charged atoms : 1896 net assigned charge : 3.988007 assigned positive charge : 290.1879 centred at (gu) : 95.55570 92.24284 89.35022 assigned negative charge : -286.2004 centred at (gu) : 95.41911 92.02898 89.32764 start vw surface at 0.1300000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 58211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19468 grid for indexing accessible points = 1.400000 m= 21154 mr = 38412 m= 3675 mr = 15218 m= 250 mr = 2337 m= 2 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 27209 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 14932 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) : 0.6255491 object centre at (A) : 27.54800 4.033501 113.5055 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4172859E-02 6.6550053E-03 midg,1,midg; midg,igrid,midg -1.2872643E-03 2.9767880E-03 1,midg,midg; igrid,midg,midg 4.3085232E-02 3.1841736E-02 gauss-seidel spectral radius is 0.9985460 estimated iterations to convergence 208 setup time was (sec) 0.7200000 now iterating at: 11:39:32 rms-change max change #iterations 3.473305 162.2364 at 10iterations 1.581200 61.67839 at 20iterations 0.7203380 24.96208 at 30iterations 0.3281142 11.64658 at 40iterations 0.1497633 5.432209 at 50iterations 6.8443187E-02 2.582783 at 60iterations 3.1186564E-02 1.075415 at 70iterations 1.4178692E-02 0.5025263 at 80iterations 6.5021999E-03 0.2403736 at 90iterations 2.9638293E-03 0.1034889 at 100iterations 1.3543124E-03 4.8990011E-02 at 110iterations 6.1986747E-04 2.5924683E-02 at 120iterations finished qdiffx linear iterations at : 11:39:39 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 6.1986747E-04 2.5924683E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 11:39:39 7.464u 0.232s 0:08.00 96.1% 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 Sun Oct 9 2011 at 11:39:39 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 !!! WARNING: ASP 359 has a net charge of -1.0260 !!! WARNING: HIR 475 has a net charge of 0.5140 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: 2.814971 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): -0.9070000 56.00300 ymin,ymax (A): -19.48500 27.55200 zmin,zma (A): 93.57300 133.4380 x,y,z range (A): 56.91000 47.03700 39.86499 scale (grids/A): 2.814971 object centre (A): 27.54800 4.033501 113.5055 number of atom coordinates read : 1956 total number of charged atoms : 1896 net assigned charge : 3.988007 assigned positive charge : 290.1879 centred at (gu) : 98.33339 93.36435 89.02519 assigned negative charge : -286.2004 centred at (gu) : 98.12876 93.04346 88.99155 start vw surface at 0.1300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 134552 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19468 grid for indexing accessible points = 1.400000 m= 66573 mr = 93610 m= 25522 mr = 53223 m= 6729 mr = 20316 m= 1082 mr = 5190 m= 63 mr = 767 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.050000 number of dielectric boundary points 61394 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 15167 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) : 1.876647 object centre at (A) : 27.54800 4.033501 113.5055 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1774159 7.7229388E-02 midg,1,midg; midg,igrid,midg 7.1739629E-02 6.7325388E-03 1,midg,midg; igrid,midg,midg 0.9825040 0.3309698 gauss-seidel spectral radius is 0.9992347 estimated iterations to convergence 285 setup time was (sec) 1.350000 now iterating at: 11:39:41 rms-change max change #iterations 8.299056 276.0151 at 10iterations 4.804972 125.7866 at 20iterations 2.766454 71.41893 at 30iterations 1.583218 34.72105 at 40iterations 0.9076462 21.83750 at 50iterations 0.5184464 11.78775 at 60iterations 0.2961006 6.583737 at 70iterations 0.1686170 3.670514 at 80iterations 9.6048631E-02 2.062225 at 90iterations 5.4665286E-02 1.180063 at 100iterations 3.1188637E-02 0.6262436 at 110iterations 1.7727628E-02 0.3614991 at 120iterations 1.0092520E-02 0.2315216 at 130iterations 5.7385783E-03 0.1315079 at 140iterations 3.2509484E-03 6.5740466E-02 at 150iterations 1.8512380E-03 3.8383961E-02 at 160iterations 1.0524240E-03 2.2251487E-02 at 170iterations 5.9665705E-04 1.2069702E-02 at 180iterations finished qdiffx linear iterations at : 11:39:51 total time elapsed so far: 11.71000 # loops : 180 mean,max change (kT/e) : 5.9665705E-04 1.2069702E-02 energy calculations done at 11.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.87000 DelPhi exited at 11:39:52 11.875u 0.235s 0:12.42 97.4% 0+0k 0+0io 0pf+0w