Sat Oct 15 13:28:48 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 15 2011 at 13:28:48 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5510 !!! WARNING: HIR 122 has a net charge of 0.5140 !!! WARNING: HIR 123 has a net charge of 0.5140 !!! WARNING: HIR 160 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4861927 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): -8.608000 49.90900 ymin,ymax (A): -6.503000 66.71900 zmin,zma (A): -11.09100 52.68600 x,y,z range (A): 58.51700 73.22200 63.77700 scale (grids/A): 0.4861927 object centre (A): 20.65050 30.10800 20.79750 number of atom coordinates read : 5510 total number of charged atoms : 5356 net assigned charge : -13.95799 assigned positive charge : 823.4017 centred at (gu) : 89.78487 89.82888 89.96396 assigned negative charge : -837.3670 centred at (gu) : 89.81991 89.98009 90.00555 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7905 nv = 96 ne = 84 npr = 114025 no. pairs analyzed = 114025 no. exposed pairs = 6953 no. arc points = 46598 no. surface atoms = 2358 nbur = 3152 mkacc time = 0.3000000 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 = 1.736000 m= 227 mr = 3991 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 4138 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4388 ## 677 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 10903 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1624778E-11 -1.0509055E-10 midg,1,midg; midg,igrid,midg 9.1609678E-11 -2.1058430E-10 1,midg,midg; igrid,midg,midg -2.9609284E-11 -9.3732702E-11 gauss-seidel spectral radius is 0.9784222 estimated iterations to convergence 56 setup time was (sec) 0.8800000 now iterating at: 13:28:49 rms-change max change #iterations 5.8054391E-02 8.891090 at 10iterations 3.5675247E-03 0.5581665 at 20iterations 5.4039626E-04 8.3598137E-02 at 30iterations 1.6380365E-04 2.2121429E-02 at 40iterations 6.0504248E-05 9.5796585E-03 at 50iterations finished qdiffx linear iterations at : 13:28:57 total time elapsed so far: 5.760000 # loops : 50 mean,max change (kT/e) : 6.0504248E-05 9.5796585E-03 energy calculations done at 5.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.920000 DelPhi exited at 13:28:59 5.926u 0.439s 0:11.56 54.9% 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 15 2011 at 13:29:00 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5510 !!! WARNING: HIR 122 has a net charge of 0.5140 !!! WARNING: HIR 123 has a net charge of 0.5140 !!! WARNING: HIR 160 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.458578 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): -8.608000 49.90900 ymin,ymax (A): -6.503000 66.71900 zmin,zma (A): -11.09100 52.68600 x,y,z range (A): 58.51700 73.22200 63.77700 scale (grids/A): 1.458578 object centre (A): 20.65050 30.10800 20.79750 number of atom coordinates read : 5510 total number of charged atoms : 5356 net assigned charge : -13.95799 assigned positive charge : 823.4017 centred at (gu) : 89.35282 89.48444 89.89004 assigned negative charge : -837.3670 centred at (gu) : 89.45959 89.93980 90.01654 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 90975 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46598 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 24580 mr = 62171 m= 1812 mr = 15549 m= 37 mr = 692 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 38993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 591 ## 16 charges are in solution ## iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 39538 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) : 0.4861927 object centre at (A) : 20.65050 30.10800 20.79750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0851327E-03 -1.1407129E-02 midg,1,midg; midg,igrid,midg 5.4809703E-03 -2.2252925E-02 1,midg,midg; igrid,midg,midg -1.3708044E-03 -6.0930178E-03 gauss-seidel spectral radius is 0.9979469 estimated iterations to convergence 176 setup time was (sec) 1.220000 now iterating at: 13:29:03 rms-change max change #iterations 3.684924 140.1654 at 10iterations 1.456432 54.07974 at 20iterations 0.5749868 20.53300 at 30iterations 0.2270009 7.314231 at 40iterations 8.9950368E-02 3.312386 at 50iterations 3.5524186E-02 1.065059 at 60iterations 1.4130572E-02 0.4386415 at 70iterations 5.6416499E-03 0.2015457 at 80iterations 2.2958198E-03 7.3730469E-02 at 90iterations 9.6326455E-04 3.1791687E-02 at 100iterations 4.3708654E-04 1.6508102E-02 at 110iterations 2.2783142E-04 7.2517395E-03 at 120iterations finished qdiffx linear iterations at : 13:29:32 total time elapsed so far: 14.14000 # loops : 120 mean,max change (kT/e) : 2.2783142E-04 7.2517395E-03 energy calculations done at 14.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.31000 DelPhi exited at 13:29:32 14.318u 0.514s 0:31.99 46.3% 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 13:29:32 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5510 !!! WARNING: HIR 122 has a net charge of 0.5140 !!! WARNING: HIR 123 has a net charge of 0.5140 !!! WARNING: HIR 160 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.187867 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): -8.608000 49.90900 ymin,ymax (A): -6.503000 66.71900 zmin,zma (A): -11.09100 52.68600 x,y,z range (A): 58.51700 73.22200 63.77700 scale (grids/A): 2.187867 object centre (A): 20.65050 30.10800 20.79750 number of atom coordinates read : 5510 total number of charged atoms : 5356 net assigned charge : -13.95799 assigned positive charge : 823.4017 centred at (gu) : 89.02858 89.22626 89.83473 assigned negative charge : -837.3670 centred at (gu) : 89.18932 89.90968 90.02494 start vw surface at 0.1900000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 212696 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46598 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 90566 mr = 154148 m= 20820 mr = 68846 m= 2432 mr = 14272 m= 100 mr = 1381 m= 0 mr = 15 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.940000 number of dielectric boundary points 87952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 42665 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) : 1.458578 object centre at (A) : 20.65050 30.10800 20.79750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3467804E-02 -0.2268632 midg,1,midg; midg,igrid,midg -3.5701741E-02 -0.4750537 1,midg,midg; igrid,midg,midg -4.3420654E-02 -0.1253129 gauss-seidel spectral radius is 0.9991270 estimated iterations to convergence 267 setup time was (sec) 2.360000 now iterating at: 13:29:36 rms-change max change #iterations 10.42212 303.2802 at 10iterations 5.973820 145.0548 at 20iterations 3.382378 71.71699 at 30iterations 1.898851 41.06407 at 40iterations 1.064830 25.55131 at 50iterations 0.5920197 12.33978 at 60iterations 0.3286054 6.819160 at 70iterations 0.1817095 3.804443 at 80iterations 0.1004388 2.100397 at 90iterations 5.5429097E-02 1.278177 at 100iterations 3.0562701E-02 0.5813293 at 110iterations 1.6780220E-02 0.3410339 at 120iterations 9.2423949E-03 0.1683426 at 130iterations 5.0907186E-03 9.1945648E-02 at 140iterations 2.8028996E-03 5.1262856E-02 at 150iterations 1.5466471E-03 2.9848099E-02 at 160iterations 8.5471605E-04 1.6420364E-02 at 170iterations 4.7824116E-04 8.3618164E-03 at 180iterations finished qdiffx linear iterations at : 13:30:00 total time elapsed so far: 24.37000 # loops : 180 mean,max change (kT/e) : 4.7824116E-04 8.3618164E-03 energy calculations done at 24.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.54000 DelPhi exited at 13:30:00 24.548u 0.577s 0:27.93 89.9% 0+0k 0+0io 0pf+0w