Sat Oct 8 16:40:55 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 16:40:55 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4556 !!! WARNING: GLM 204 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5456691 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): 21.41700 79.64900 ymin,ymax (A): 119.0690 184.3100 zmin,zma (A): -2.111000 59.77300 x,y,z range (A): 58.23200 65.24100 61.88400 scale (grids/A): 0.5456691 object centre (A): 50.53300 151.6895 28.83100 number of atom coordinates read : 4556 total number of charged atoms : 4382 net assigned charge : 4.906037 assigned positive charge : 695.4215 centred at (gu) : 90.62135 89.44208 87.42765 assigned negative charge : -690.5188 centred at (gu) : 90.62001 89.39400 87.47197 start vw surface at 0.1900000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8707 nv = 96 ne = 84 npr = 92033 no. pairs analyzed = 92033 no. exposed pairs = 5669 no. arc points = 38789 no. surface atoms = 1879 nbur = 2677 mkacc time = 0.2000000 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 = 1.568000 m= 408 mr = 4648 m= 0 mr = 19 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.4500000 number of dielectric boundary points 4448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3954 ## 513 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 11563 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4015541E-09 -8.0594205E-11 midg,1,midg; midg,igrid,midg -2.3246934E-10 6.7302325E-10 1,midg,midg; igrid,midg,midg 2.3768112E-10 3.5152797E-10 gauss-seidel spectral radius is 0.9828002 estimated iterations to convergence 63 setup time was (sec) 0.7200000 now iterating at: 16:40:56 rms-change max change #iterations 9.0684690E-02 14.24047 at 10iterations 7.5043957E-03 1.121372 at 20iterations 2.1796084E-03 0.3680534 at 30iterations 1.1007112E-03 0.1858406 at 40iterations 5.6306901E-04 9.4425201E-02 at 50iterations finished qdiffx linear iterations at : 16:40:59 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 5.6306901E-04 9.4425201E-02 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 16:41:00 4.332u 0.231s 0:04.86 93.8% 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 16:41:00 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4556 !!! WARNING: GLM 204 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.637007 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): 21.41700 79.64900 ymin,ymax (A): 119.0690 184.3100 zmin,zma (A): -2.111000 59.77300 x,y,z range (A): 58.23200 65.24100 61.88400 scale (grids/A): 1.637007 object centre (A): 50.53300 151.6895 28.83100 number of atom coordinates read : 4556 total number of charged atoms : 4382 net assigned charge : 4.906037 assigned positive charge : 695.4215 centred at (gu) : 91.86298 88.32489 82.28187 assigned negative charge : -690.5188 centred at (gu) : 91.85991 88.18167 82.41559 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 97582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38789 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31694 mr = 68269 m= 3680 mr = 21776 m= 135 mr = 1917 m= 0 mr = 18 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 645 time to turn everything in is 0.7300000 number of dielectric boundary points 41111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 483 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 33594 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) : 0.5456691 object centre at (A) : 50.53300 151.6895 28.83100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1357811E-03 9.9700559E-03 midg,1,midg; midg,igrid,midg 1.5971579E-02 3.3548839E-02 1,midg,midg; igrid,midg,midg -1.3496944E-02 -1.1739132E-02 gauss-seidel spectral radius is 0.9983490 estimated iterations to convergence 195 setup time was (sec) 1.060000 now iterating at: 16:41:01 rms-change max change #iterations 4.300117 179.2400 at 10iterations 1.861481 67.86845 at 20iterations 0.8058185 26.21265 at 30iterations 0.3518388 10.74827 at 40iterations 0.1530672 4.748807 at 50iterations 6.6981971E-02 1.969081 at 60iterations 2.9461142E-02 1.017995 at 70iterations 1.3285839E-02 0.4093647 at 80iterations 6.4417496E-03 0.2291737 at 90iterations 3.5588371E-03 0.1236916 at 100iterations 2.3192803E-03 8.1085205E-02 at 110iterations 1.6945951E-03 5.8177948E-02 at 120iterations finished qdiffx linear iterations at : 16:41:10 total time elapsed so far: 9.790000 # loops : 120 mean,max change (kT/e) : 1.6945951E-03 5.8177948E-02 energy calculations done at 9.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.970000 DelPhi exited at 16:41:10 9.973u 0.264s 0:10.57 96.7% 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 8 2011 at 16:41:11 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4556 !!! WARNING: GLM 204 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.455511 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): 21.41700 79.64900 ymin,ymax (A): 119.0690 184.3100 zmin,zma (A): -2.111000 59.77300 x,y,z range (A): 58.23200 65.24100 61.88400 scale (grids/A): 2.455511 object centre (A): 50.53300 151.6895 28.83100 number of atom coordinates read : 4556 total number of charged atoms : 4382 net assigned charge : 4.906037 assigned positive charge : 695.4215 centred at (gu) : 92.79398 87.48696 78.42265 assigned negative charge : -690.5188 centred at (gu) : 92.78976 87.27254 78.62328 start vw surface at 0.1900000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 227283 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38789 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 108970 mr = 167583 m= 32668 mr = 86365 m= 5978 mr = 24390 m= 497 mr = 4025 m= 12 mr = 244 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 2311 time to turn everything in is 1.820000 number of dielectric boundary points 92801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 35022 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) : 1.637007 object centre at (A) : 50.53300 151.6895 28.83100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2719380E-03 0.2178291 midg,1,midg; midg,igrid,midg 0.2194805 0.6091633 1,midg,midg; igrid,midg,midg -0.2165307 -0.2160761 gauss-seidel spectral radius is 0.9992239 estimated iterations to convergence 283 setup time was (sec) 2.180000 now iterating at: 16:41:13 rms-change max change #iterations 11.09672 275.8385 at 10iterations 6.481588 136.5017 at 20iterations 3.753879 79.18773 at 30iterations 2.167408 46.92858 at 40iterations 1.247816 26.92029 at 50iterations 0.7152148 12.73472 at 60iterations 0.4100222 7.246637 at 70iterations 0.2340507 4.114849 at 80iterations 0.1335653 2.799268 at 90iterations 7.6320946E-02 1.299429 at 100iterations 4.3543562E-02 0.7942467 at 110iterations 2.4999205E-02 0.4468689 at 120iterations 1.4453368E-02 0.2645035 at 130iterations 8.4847873E-03 0.1823387 at 140iterations 5.1832343E-03 0.1006393 at 150iterations 3.3614712E-03 7.8868866E-02 at 160iterations 2.3624448E-03 5.1548004E-02 at 170iterations 1.7991031E-03 3.7946701E-02 at 180iterations finished qdiffx linear iterations at : 16:41:27 total time elapsed so far: 16.45000 # loops : 180 mean,max change (kT/e) : 1.7991031E-03 3.7946701E-02 energy calculations done at 16.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.63000 DelPhi exited at 16:41:28 16.636u 0.307s 0:17.25 98.1% 0+0k 0+0io 0pf+0w