Sat Oct 8 19:53:37 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 19:53:37 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2558 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 477 has a net charge of 1.4000 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: 0.6186678 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): -31.89400 17.35400 ymin,ymax (A): -24.27300 22.99300 zmin,zma (A): -12.50300 45.04000 x,y,z range (A): 49.24800 47.26600 57.54300 scale (grids/A): 0.6186678 object centre (A): -7.270000 -0.6399994 16.26850 number of atom coordinates read : 2558 total number of charged atoms : 2470 net assigned charge : 4.000009 assigned positive charge : 394.2340 centred at (gu) : 88.57444 89.42867 89.81280 assigned negative charge : -390.2346 centred at (gu) : 88.47424 89.46527 89.69839 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6462 nv = 96 ne = 84 npr = 52019 no. pairs analyzed = 52019 no. exposed pairs = 3025 no. arc points = 21853 no. surface atoms = 1020 nbur = 1538 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3600 m= 0 mr = 27 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.2100000 number of dielectric boundary points 3154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2148 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8079 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4262154E-09 1.0016452E-08 midg,1,midg; midg,igrid,midg 6.2723298E-09 7.5643514E-10 1,midg,midg; igrid,midg,midg -4.6398982E-09 6.9874746E-09 gauss-seidel spectral radius is 0.9864650 estimated iterations to convergence 70 setup time was (sec) 0.4400000 now iterating at: 19:53:38 rms-change max change #iterations 0.1252374 19.04327 at 10iterations 1.1607581E-02 1.536905 at 20iterations 1.0846336E-03 0.1624269 at 30iterations 1.1402828E-04 2.1865845E-02 at 40iterations 1.3662913E-05 2.6702881E-03 at 50iterations finished qdiffx linear iterations at : 19:53:43 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 1.3662913E-05 2.6702881E-03 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 19:53:43 3.637u 0.406s 0:05.93 67.9% 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 8 2011 at 19:53:43 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2558 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 477 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.856003 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): -31.89400 17.35400 ymin,ymax (A): -24.27300 22.99300 zmin,zma (A): -12.50300 45.04000 x,y,z range (A): 49.24800 47.26600 57.54300 scale (grids/A): 1.856003 object centre (A): -7.270000 -0.6399994 16.26850 number of atom coordinates read : 2558 total number of charged atoms : 2470 net assigned charge : 4.000009 assigned positive charge : 394.2340 centred at (gu) : 85.72295 88.28563 89.43791 assigned negative charge : -390.2346 centred at (gu) : 85.42233 88.39553 89.09515 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70129 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21853 grid for indexing accessible points = 1.400000 m= 23910 mr = 48695 m= 3402 mr = 17507 m= 151 mr = 2052 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 4571 time to turn everything in is 0.3400000 number of dielectric boundary points 29304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19383 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) : 0.6186678 object centre at (A) : -7.270000 -0.6399994 16.26850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6384391E-02 2.8629173E-02 midg,1,midg; midg,igrid,midg 1.2436063E-02 3.4470982E-03 1,midg,midg; igrid,midg,midg -4.4280435E-03 3.5585385E-02 gauss-seidel spectral radius is 0.9985594 estimated iterations to convergence 209 setup time was (sec) 0.5900000 now iterating at: 19:53:45 rms-change max change #iterations 4.031711 175.9878 at 10iterations 1.853511 59.68405 at 20iterations 0.8456783 30.75954 at 30iterations 0.3891100 12.88486 at 40iterations 0.1789566 6.660301 at 50iterations 8.1926472E-02 3.078257 at 60iterations 3.7781429E-02 1.353951 at 70iterations 1.7320894E-02 0.5412803 at 80iterations 7.9445848E-03 0.2657852 at 90iterations 3.6499896E-03 0.1251373 at 100iterations 1.6707013E-03 5.8086395E-02 at 110iterations 7.7144499E-04 2.7000427E-02 at 120iterations finished qdiffx linear iterations at : 19:53:56 total time elapsed so far: 8.150000 # loops : 120 mean,max change (kT/e) : 7.7144499E-04 2.7000427E-02 energy calculations done at 8.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.280000 DelPhi exited at 19:53:56 8.280u 0.805s 0:12.91 70.3% 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 8 2011 at 19:53:56 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2558 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 477 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.784005 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): -31.89400 17.35400 ymin,ymax (A): -24.27300 22.99300 zmin,zma (A): -12.50300 45.04000 x,y,z range (A): 49.24800 47.26600 57.54300 scale (grids/A): 2.784005 object centre (A): -7.270000 -0.6399994 16.26850 number of atom coordinates read : 2558 total number of charged atoms : 2470 net assigned charge : 4.000009 assigned positive charge : 394.2340 centred at (gu) : 83.58439 87.42831 89.15687 assigned negative charge : -390.2346 centred at (gu) : 83.13353 87.59322 88.64252 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 162399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21853 grid for indexing accessible points = 1.400000 m= 79830 mr = 118158 m= 26706 mr = 65378 m= 5918 mr = 21324 m= 665 mr = 4330 m= 20 mr = 413 m= 0 mr = 3 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 15738 time to turn everything in is 0.9700000 number of dielectric boundary points 65932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 19758 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) : 1.856003 object centre at (A) : -7.270000 -0.6399994 16.26850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4917056E-02 0.3347507 midg,1,midg; midg,igrid,midg 0.1617446 1.7363779E-02 1,midg,midg; igrid,midg,midg -3.6603767E-02 0.4689126 gauss-seidel spectral radius is 0.9992341 estimated iterations to convergence 285 setup time was (sec) 1.230000 now iterating at: 19:53:58 rms-change max change #iterations 9.513290 319.5966 at 10iterations 5.469327 109.7863 at 20iterations 3.128492 69.15346 at 30iterations 1.784598 39.02856 at 40iterations 1.016464 21.54841 at 50iterations 0.5805363 11.82451 at 60iterations 0.3299123 6.296288 at 70iterations 0.1882264 3.716614 at 80iterations 0.1070206 2.151660 at 90iterations 6.0936224E-02 1.244295 at 100iterations 3.4779269E-02 0.6873543 at 110iterations 1.9856695E-02 0.3655052 at 120iterations 1.1289543E-02 0.2161293 at 130iterations 6.4490777E-03 0.1603222 at 140iterations 3.6897603E-03 7.3345184E-02 at 150iterations 2.1230767E-03 4.0073395E-02 at 160iterations 1.2332543E-03 2.7801514E-02 at 170iterations 7.2437566E-04 1.7839432E-02 at 180iterations finished qdiffx linear iterations at : 19:54:16 total time elapsed so far: 13.35000 # loops : 180 mean,max change (kT/e) : 7.2437566E-04 1.7839432E-02 energy calculations done at 13.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.49000 DelPhi exited at 19:54:16 13.496u 1.175s 0:19.99 73.3% 0+0k 0+0io 0pf+0w