Mon Oct 10 14:17:46 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 14:17:46 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5852472 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): 19.61400 80.44300 ymin,ymax (A): -24.70900 33.28700 zmin,zma (A): -33.83600 22.76100 x,y,z range (A): 60.82900 57.99600 56.59700 scale (grids/A): 0.5852472 object centre (A): 50.02850 4.289000 -5.537501 number of atom coordinates read : 2976 total number of charged atoms : 2832 net assigned charge : -1.999984 assigned positive charge : 460.8610 centred at (gu) : 89.70032 89.31219 91.55461 assigned negative charge : -462.8621 centred at (gu) : 89.76974 89.32031 91.60483 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6879 nv = 96 ne = 84 npr = 57164 no. pairs analyzed = 57164 no. exposed pairs = 4167 no. arc points = 29392 no. surface atoms = 1386 nbur = 1590 mkacc time = 8.9999996E-02 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 = 1.456000 m= 343 mr = 3385 m= 6 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2941 ## 297 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8628 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8389166E-10 -2.7072613E-09 midg,1,midg; midg,igrid,midg -3.3099296E-10 -6.2112421E-10 1,midg,midg; igrid,midg,midg 1.4663204E-09 -2.2432551E-09 gauss-seidel spectral radius is 0.9849381 estimated iterations to convergence 67 setup time was (sec) 0.4000000 now iterating at: 14:17:47 rms-change max change #iterations 0.1036059 17.51157 at 10iterations 8.2869036E-03 1.438665 at 20iterations 6.6038058E-04 8.7047577E-02 at 30iterations 5.4060358E-05 8.7337494E-03 at 40iterations 4.4775520E-06 6.8664551E-04 at 50iterations finished qdiffx linear iterations at : 14:17:50 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 4.4775520E-06 6.8664551E-04 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 14:17:50 3.371u 0.173s 0:03.87 91.4% 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 14:17:50 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.755741 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): 19.61400 80.44300 ymin,ymax (A): -24.70900 33.28700 zmin,zma (A): -33.83600 22.76100 x,y,z range (A): 60.82900 57.99600 56.59700 scale (grids/A): 1.755741 object centre (A): 50.02850 4.289000 -5.537501 number of atom coordinates read : 2976 total number of charged atoms : 2832 net assigned charge : -1.999984 assigned positive charge : 460.8610 centred at (gu) : 89.10049 87.93596 94.66325 assigned negative charge : -462.8621 centred at (gu) : 89.30894 87.96068 94.81401 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29392 grid for indexing accessible points = 1.400000 m= 24881 mr = 49406 m= 3256 mr = 16745 m= 108 mr = 1843 m= 0 mr = 23 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 34845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 298 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 21988 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) : 0.5852472 object centre at (A) : 50.02850 4.289000 -5.537501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1210097E-03 2.2135682E-02 midg,1,midg; midg,igrid,midg 1.8099241E-02 2.3436951E-03 1,midg,midg; igrid,midg,midg -2.4645211E-02 -3.8083546E-02 gauss-seidel spectral radius is 0.9984507 estimated iterations to convergence 202 setup time was (sec) 0.5700000 now iterating at: 14:17:51 rms-change max change #iterations 3.984285 183.2985 at 10iterations 1.764141 65.69330 at 20iterations 0.7815954 26.97581 at 30iterations 0.3478874 11.35933 at 40iterations 0.1549788 5.581459 at 50iterations 6.8943717E-02 2.293821 at 60iterations 3.0704577E-02 1.117212 at 70iterations 1.3643250E-02 0.4761715 at 80iterations 6.0989973E-03 0.1931362 at 90iterations 2.7142544E-03 9.6444607E-02 at 100iterations 1.2106028E-03 4.0954590E-02 at 110iterations 5.4009358E-04 1.8391609E-02 at 120iterations finished qdiffx linear iterations at : 14:17:58 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 5.4009358E-04 1.8391609E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 14:17:58 7.711u 0.206s 0:08.38 94.3% 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 Mon Oct 10 2011 at 14:17:58 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.633612 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): 19.61400 80.44300 ymin,ymax (A): -24.70900 33.28700 zmin,zma (A): -33.83600 22.76100 x,y,z range (A): 60.82900 57.99600 56.59700 scale (grids/A): 2.633612 object centre (A): 50.02850 4.289000 -5.537501 number of atom coordinates read : 2976 total number of charged atoms : 2832 net assigned charge : -1.999984 assigned positive charge : 460.8610 centred at (gu) : 88.65043 86.90386 96.99458 assigned negative charge : -462.8621 centred at (gu) : 88.96328 86.94098 97.22105 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 172877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29392 grid for indexing accessible points = 1.400000 m= 82128 mr = 120706 m= 26685 mr = 63855 m= 5493 mr = 20103 m= 547 mr = 3877 m= 13 mr = 308 m= 0 mr = 2 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 78892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 22651 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) : 1.755741 object centre at (A) : 50.02850 4.289000 -5.537501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1139130 0.2829435 midg,1,midg; midg,igrid,midg 0.4461295 3.7362374E-02 1,midg,midg; igrid,midg,midg -0.3492169 -0.3614374 gauss-seidel spectral radius is 0.9992223 estimated iterations to convergence 283 setup time was (sec) 1.150000 now iterating at: 14:18:00 rms-change max change #iterations 9.823712 272.0737 at 10iterations 5.716422 135.4955 at 20iterations 3.281380 62.83616 at 30iterations 1.880993 40.22688 at 40iterations 1.080437 21.36542 at 50iterations 0.6149846 12.10285 at 60iterations 0.3500651 7.593023 at 70iterations 0.1987041 3.898922 at 80iterations 0.1132338 2.060966 at 90iterations 6.4215548E-02 1.263905 at 100iterations 3.6337715E-02 0.6848049 at 110iterations 2.0605633E-02 0.4049835 at 120iterations 1.1664545E-02 0.2398010 at 130iterations 6.6254484E-03 0.1286317 at 140iterations 3.7453042E-03 6.5963745E-02 at 150iterations 2.1228080E-03 3.9985657E-02 at 160iterations 1.1996023E-03 2.4055481E-02 at 170iterations 6.8156712E-04 1.3038635E-02 at 180iterations finished qdiffx linear iterations at : 14:18:11 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 6.8156712E-04 1.3038635E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 14:18:12 12.531u 0.206s 0:13.09 97.2% 0+0k 0+0io 0pf+0w