Mon Oct 10 21:09:53 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 Mon Oct 10 2011 at 21:09:53 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2542 !!! WARNING: HIR 103 has a net charge of 0.5140 !!! WARNING: HIR 229 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: 0.6318555 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): -10.14300 45.36800 ymin,ymax (A): 28.20500 81.35300 zmin,zma (A): -10.60700 45.73500 x,y,z range (A): 55.51100 53.14800 56.34200 scale (grids/A): 0.6318555 object centre (A): 17.61250 54.77900 17.56400 number of atom coordinates read : 2542 total number of charged atoms : 2405 net assigned charge : -0.9719932 assigned positive charge : 378.0029 centred at (gu) : 89.01573 90.76799 89.64220 assigned negative charge : -378.9760 centred at (gu) : 88.98214 90.83862 89.59450 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7044 nv = 96 ne = 84 npr = 49965 no. pairs analyzed = 49965 no. exposed pairs = 3549 no. arc points = 25632 no. surface atoms = 1175 nbur = 1367 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 400 mr = 3451 m= 7 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.2800000 number of dielectric boundary points 3932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2542 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8327 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7987792E-09 3.0506027E-09 midg,1,midg; midg,igrid,midg 4.5200954E-09 -8.8486765E-09 1,midg,midg; igrid,midg,midg -5.0465307E-09 1.6290800E-09 gauss-seidel spectral radius is 0.9870382 estimated iterations to convergence 72 setup time was (sec) 0.5200000 now iterating at: 21:09:54 rms-change max change #iterations 0.1336375 20.66572 at 10iterations 1.3001963E-02 2.134302 at 20iterations 1.2685370E-03 0.2025161 at 30iterations 1.2612762E-04 1.8844604E-02 at 40iterations 1.3551911E-05 2.0923615E-03 at 50iterations finished qdiffx linear iterations at : 21:09:57 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 1.3551911E-05 2.0923615E-03 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 21:09:57 3.248u 0.197s 0:03.83 89.5% 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 Mon Oct 10 2011 at 21:09:57 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2542 !!! WARNING: HIR 103 has a net charge of 0.5140 !!! WARNING: HIR 229 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: 1.895566 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): -10.14300 45.36800 ymin,ymax (A): 28.20500 81.35300 zmin,zma (A): -10.60700 45.73500 x,y,z range (A): 55.51100 53.14800 56.34200 scale (grids/A): 1.895566 object centre (A): 17.61250 54.77900 17.56400 number of atom coordinates read : 2542 total number of charged atoms : 2405 net assigned charge : -0.9719932 assigned positive charge : 378.0029 centred at (gu) : 87.04641 92.30346 88.92616 assigned negative charge : -378.9760 centred at (gu) : 86.94659 92.51597 88.78341 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 75775 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25632 grid for indexing accessible points = 1.400000 m= 26404 mr = 49399 m= 4322 mr = 18404 m= 257 mr = 2561 m= 1 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1936 time to turn everything in is 0.5300000 number of dielectric boundary points 36306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 18917 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) : 0.6318555 object centre at (A) : 17.61250 54.77900 17.56400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8136569E-03 -1.1664062E-02 midg,1,midg; midg,igrid,midg 1.8510414E-02 -2.4331896E-02 1,midg,midg; igrid,midg,midg -4.0027020E-03 3.1241688E-03 gauss-seidel spectral radius is 0.9986431 estimated iterations to convergence 215 setup time was (sec) 0.8200000 now iterating at: 21:09:58 rms-change max change #iterations 4.202454 168.9962 at 10iterations 1.964244 73.14862 at 20iterations 0.9186319 28.53555 at 30iterations 0.4300204 13.62610 at 40iterations 0.2013680 6.677378 at 50iterations 9.4333075E-02 2.920462 at 60iterations 4.4150379E-02 1.405050 at 70iterations 2.0695541E-02 0.7054601 at 80iterations 9.7091859E-03 0.2997112 at 90iterations 4.5476179E-03 0.1341295 at 100iterations 2.1335797E-03 7.1651459E-02 at 110iterations 9.9681329E-04 3.7368774E-02 at 120iterations finished qdiffx linear iterations at : 21:10:05 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 9.9681329E-04 3.7368774E-02 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.420000 DelPhi exited at 21:10:05 7.427u 0.225s 0:07.98 95.7% 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 Mon Oct 10 2011 at 21:10:05 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2542 !!! WARNING: HIR 103 has a net charge of 0.5140 !!! WARNING: HIR 229 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: 2.843350 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): -10.14300 45.36800 ymin,ymax (A): 28.20500 81.35300 zmin,zma (A): -10.60700 45.73500 x,y,z range (A): 55.51100 53.14800 56.34200 scale (grids/A): 2.843350 object centre (A): 17.61250 54.77900 17.56400 number of atom coordinates read : 2542 total number of charged atoms : 2405 net assigned charge : -0.9719932 assigned positive charge : 378.0029 centred at (gu) : 85.56958 93.45535 88.38910 assigned negative charge : -378.9760 centred at (gu) : 85.41996 93.77388 88.17520 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 175103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25632 grid for indexing accessible points = 1.400000 m= 84531 mr = 120696 m= 30949 mr = 66585 m= 7736 mr = 23877 m= 1129 mr = 5611 m= 66 mr = 739 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 6455 time to turn everything in is 1.360000 number of dielectric boundary points 81981 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 19240 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) : 1.895566 object centre at (A) : 17.61250 54.77900 17.56400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1003321 -0.1087816 midg,1,midg; midg,igrid,midg 0.2243116 -0.1837962 1,midg,midg; igrid,midg,midg 0.1710776 1.1041492E-02 gauss-seidel spectral radius is 0.9992764 estimated iterations to convergence 293 setup time was (sec) 1.680000 now iterating at: 21:10:07 rms-change max change #iterations 10.04836 343.5786 at 10iterations 5.949564 160.9838 at 20iterations 3.501160 87.92459 at 30iterations 2.051449 53.49310 at 40iterations 1.195692 24.72390 at 50iterations 0.6959506 14.36685 at 60iterations 0.4055265 8.064140 at 70iterations 0.2349849 4.726609 at 80iterations 0.1363613 2.807585 at 90iterations 7.8867152E-02 1.512689 at 100iterations 4.5671206E-02 0.8082851 at 110iterations 2.6419912E-02 0.4781303 at 120iterations 1.5267790E-02 0.3032494 at 130iterations 8.8204714E-03 0.1571846 at 140iterations 5.1019532E-03 9.6687898E-02 at 150iterations 2.9526136E-03 5.6381226E-02 at 160iterations 1.7069028E-03 2.9758692E-02 at 170iterations 9.8624302E-04 1.7466545E-02 at 180iterations finished qdiffx linear iterations at : 21:10:18 total time elapsed so far: 12.10000 # loops : 180 mean,max change (kT/e) : 9.8624302E-04 1.7466545E-02 energy calculations done at 12.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 21:10:18 12.275u 0.257s 0:13.12 95.4% 0+0k 0+0io 0pf+0w