Tue Nov 22 14:09:59 PST 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+sph.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 = amb.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 Tue Nov 22 2011 at 14:10:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6438894 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): -5.251000 34.71900 ymin,ymax (A): -3.422000 49.17900 zmin,zma (A): -24.39300 30.89600 x,y,z range (A): 39.97000 52.60100 55.28900 scale (grids/A): 0.6438894 object centre (A): 14.73400 22.87850 3.251500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.66716 92.40908 90.21886 assigned negative charge : -284.8263 centred at (gu) : 90.76822 92.53846 90.17711 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5602 nv = 96 ne = 84 npr = 40319 no. pairs analyzed = 40319 no. exposed pairs = 2497 no. arc points = 17407 no. surface atoms = 840 nbur = 1124 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 290 mr = 3107 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.1700000 number of dielectric boundary points 2743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1745 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6538 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2483025E-09 9.6115214E-09 midg,1,midg; midg,igrid,midg 1.0414754E-08 -1.2369226E-08 1,midg,midg; igrid,midg,midg 1.2748965E-08 -5.1197255E-09 gauss-seidel spectral radius is 0.9874460 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 14:10:07 rms-change max change #iterations 0.1261744 18.54703 at 10iterations 1.2483514E-02 2.197020 at 20iterations 1.2462444E-03 0.2093620 at 30iterations 1.2690944E-04 2.0969391E-02 at 40iterations 1.2512638E-05 2.2201538E-03 at 50iterations finished qdiffx linear iterations at : 14:10:17 total time elapsed so far: 3.730000 # loops : 50 mean,max change (kT/e) : 1.2512638E-05 2.2201538E-03 energy calculations done at 3.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.860000 DelPhi exited at 14:10:20 3.859u 0.254s 0:17.70 23.1% 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 Tue Nov 22 2011 at 14:10:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.931668 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): -5.251000 34.71900 ymin,ymax (A): -3.422000 49.17900 zmin,zma (A): -24.39300 30.89600 x,y,z range (A): 39.97000 52.60100 55.28900 scale (grids/A): 1.931668 object centre (A): 14.73400 22.87850 3.251500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 92.00143 97.22728 90.65656 assigned negative charge : -284.8263 centred at (gu) : 92.30484 97.61559 90.53150 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59560 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17407 grid for indexing accessible points = 1.400000 m= 22302 mr = 40982 m= 3580 mr = 17018 m= 193 mr = 2434 m= 5 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 791 time to turn everything in is 0.3300000 number of dielectric boundary points 25124 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 14450 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) : 0.6438894 object centre at (A) : 14.73400 22.87850 3.251500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8279397E-02 1.0074015E-02 midg,1,midg; midg,igrid,midg 3.2370497E-02 -1.0167442E-02 1,midg,midg; igrid,midg,midg 7.4051446E-03 -5.0553228E-03 gauss-seidel spectral radius is 0.9985950 estimated iterations to convergence 211 setup time was (sec) 0.6100000 now iterating at: 14:10:30 rms-change max change #iterations 3.640998 161.8901 at 10iterations 1.685980 68.00471 at 20iterations 0.7803552 30.44504 at 30iterations 0.3624910 12.09423 at 40iterations 0.1674567 5.431444 at 50iterations 7.7086441E-02 2.605730 at 60iterations 3.5816893E-02 1.303698 at 70iterations 1.6586294E-02 0.5243149 at 80iterations 7.6819630E-03 0.2896862 at 90iterations 3.5474401E-03 0.1259804 at 100iterations 1.6481907E-03 5.7454586E-02 at 110iterations 7.6424173E-04 2.9640198E-02 at 120iterations finished qdiffx linear iterations at : 14:10:55 total time elapsed so far: 8.810000 # loops : 120 mean,max change (kT/e) : 7.6424173E-04 2.9640198E-02 energy calculations done at 8.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.940000 DelPhi exited at 14:10:56 8.940u 0.310s 0:31.90 28.9% 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 Tue Nov 22 2011 at 14:10:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.897502 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): -5.251000 34.71900 ymin,ymax (A): -3.422000 49.17900 zmin,zma (A): -24.39300 30.89600 x,y,z range (A): 39.97000 52.60100 55.28900 scale (grids/A): 2.897502 object centre (A): 14.73400 22.87850 3.251500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 93.00217 100.8410 90.98494 assigned negative charge : -284.8263 centred at (gu) : 93.45731 101.4235 90.79723 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 137452 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17407 grid for indexing accessible points = 1.400000 m= 71046 mr = 99105 m= 27166 mr = 58961 m= 6574 mr = 22539 m= 876 mr = 5282 m= 54 mr = 600 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 2475 time to turn everything in is 0.8200000 number of dielectric boundary points 56647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 14652 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) : 1.931668 object centre at (A) : 14.73400 22.87850 3.251500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.078829 2.1323774E-02 midg,1,midg; midg,igrid,midg 0.3221785 -0.1305043 1,midg,midg; igrid,midg,midg 3.4857236E-02 -2.9179430E-02 gauss-seidel spectral radius is 0.9992353 estimated iterations to convergence 285 setup time was (sec) 1.080000 now iterating at: 14:11:05 rms-change max change #iterations 8.576280 379.1356 at 10iterations 4.930171 117.3553 at 20iterations 2.811782 62.59874 at 30iterations 1.599266 33.14379 at 40iterations 0.9107747 18.39398 at 50iterations 0.5179018 10.91215 at 60iterations 0.2949065 6.120120 at 70iterations 0.1674824 3.638855 at 80iterations 9.4892703E-02 1.973194 at 90iterations 5.3788431E-02 1.128281 at 100iterations 3.0536970E-02 0.6101074 at 110iterations 1.7392142E-02 0.3331356 at 120iterations 9.8442491E-03 0.2063560 at 130iterations 5.6021181E-03 0.1163826 at 140iterations 3.1775369E-03 6.8059206E-02 at 150iterations 1.8024071E-03 3.3087730E-02 at 160iterations 1.0257453E-03 1.8951416E-02 at 170iterations 5.8347179E-04 1.1728644E-02 at 180iterations finished qdiffx linear iterations at : 14:11:45 total time elapsed so far: 14.57000 # loops : 180 mean,max change (kT/e) : 5.8347179E-04 1.1728644E-02 energy calculations done at 14.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.70000 DelPhi exited at 14:11:48 14.706u 0.291s 0:49.83 30.0% 0+0k 0+0io 0pf+0w