Mon Oct 10 10:31:03 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 10:31:03 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2837 !!! WARNING: HIT 233 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5607713 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): -20.45700 43.02700 ymin,ymax (A): -9.371000 45.67200 zmin,zma (A): -1.849000 53.17700 x,y,z range (A): 63.48399 55.04300 55.02600 scale (grids/A): 0.5607713 object centre (A): 11.28500 18.15050 25.66400 number of atom coordinates read : 2837 total number of charged atoms : 2686 net assigned charge : 7.514028 assigned positive charge : 416.8719 centred at (gu) : 91.33349 90.49603 86.19667 assigned negative charge : -409.3583 centred at (gu) : 91.47804 90.56716 86.02132 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6063 nv = 96 ne = 84 npr = 54399 no. pairs analyzed = 54399 no. exposed pairs = 4235 no. arc points = 31138 no. surface atoms = 1405 nbur = 1432 mkacc time = 0.1000000 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 = 1.540000 m= 288 mr = 2684 m= 0 mr = 4 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3064 ## 351 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7709 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5013840E-09 1.0855504E-09 midg,1,midg; midg,igrid,midg 1.4508468E-09 1.9491883E-10 1,midg,midg; igrid,midg,midg 1.7186372E-09 -8.4514540E-10 gauss-seidel spectral radius is 0.9836040 estimated iterations to convergence 64 setup time was (sec) 0.3900000 now iterating at: 10:31:04 rms-change max change #iterations 8.2715161E-02 14.74086 at 10iterations 5.7795448E-03 1.087123 at 20iterations 4.3045715E-04 6.9160461E-02 at 30iterations 3.7409289E-05 5.1231384E-03 at 40iterations 5.3184358E-06 6.6852570E-04 at 50iterations finished qdiffx linear iterations at : 10:31:07 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 5.3184358E-06 6.6852570E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 10:31:07 3.381u 0.168s 0:03.82 92.6% 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 10:31:07 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2837 !!! WARNING: HIT 233 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.682314 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): -20.45700 43.02700 ymin,ymax (A): -9.371000 45.67200 zmin,zma (A): -1.849000 53.17700 x,y,z range (A): 63.48399 55.04300 55.02600 scale (grids/A): 1.682314 object centre (A): 11.28500 18.15050 25.66400 number of atom coordinates read : 2837 total number of charged atoms : 2686 net assigned charge : 7.514028 assigned positive charge : 416.8719 centred at (gu) : 93.99989 91.48753 78.58942 assigned negative charge : -409.3583 centred at (gu) : 94.43385 91.70120 78.06375 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65415 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31138 grid for indexing accessible points = 1.400000 m= 19532 mr = 40056 m= 2176 mr = 12298 m= 73 mr = 906 m= 0 mr = 8 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 33928 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 302 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 20710 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) : 0.5607713 object centre at (A) : 11.28500 18.15050 25.66400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1251579E-03 8.8373162E-03 midg,1,midg; midg,igrid,midg 1.7687492E-02 2.6039721E-03 1,midg,midg; igrid,midg,midg 1.4122509E-02 -1.5009897E-02 gauss-seidel spectral radius is 0.9982950 estimated iterations to convergence 192 setup time was (sec) 0.5500000 now iterating at: 10:31:08 rms-change max change #iterations 3.415574 142.6578 at 10iterations 1.452417 64.08705 at 20iterations 0.6192901 23.37993 at 30iterations 0.2650791 9.363561 at 40iterations 0.1131343 4.319061 at 50iterations 4.8204158E-02 1.749466 at 60iterations 2.0610044E-02 0.9093704 at 70iterations 8.8107595E-03 0.3371925 at 80iterations 3.7537396E-03 0.1400290 at 90iterations 1.6068775E-03 5.8339119E-02 at 100iterations 6.8953447E-04 2.7616560E-02 at 110iterations 2.9382107E-04 1.0787010E-02 at 120iterations finished qdiffx linear iterations at : 10:31:15 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 2.9382107E-04 1.0787010E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 10:31:16 7.705u 0.180s 0:08.15 96.6% 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 10:31:16 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2837 !!! WARNING: HIT 233 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.523471 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): -20.45700 43.02700 ymin,ymax (A): -9.371000 45.67200 zmin,zma (A): -1.849000 53.17700 x,y,z range (A): 63.48399 55.04300 55.02600 scale (grids/A): 2.523471 object centre (A): 11.28500 18.15050 25.66400 number of atom coordinates read : 2837 total number of charged atoms : 2686 net assigned charge : 7.514028 assigned positive charge : 416.8719 centred at (gu) : 95.99964 92.23112 72.88406 assigned negative charge : -409.3583 centred at (gu) : 96.65064 92.55170 72.09560 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 151874 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31138 grid for indexing accessible points = 1.400000 m= 66055 mr = 99493 m= 19553 mr = 49008 m= 3225 mr = 13930 m= 257 mr = 1874 m= 5 mr = 89 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 76576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 21464 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) : 1.682314 object centre at (A) : 11.28500 18.15050 25.66400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1311550E-02 0.1061138 midg,1,midg; midg,igrid,midg 0.3296778 -2.9652784E-02 1,midg,midg; igrid,midg,midg 0.2624705 -0.4619535 gauss-seidel spectral radius is 0.9991798 estimated iterations to convergence 276 setup time was (sec) 1.040000 now iterating at: 10:31:17 rms-change max change #iterations 9.004526 281.5160 at 10iterations 5.233664 150.4771 at 20iterations 3.015698 88.09490 at 30iterations 1.722289 49.53202 at 40iterations 0.9749551 27.72842 at 50iterations 0.5518687 13.60135 at 60iterations 0.3105685 7.506417 at 70iterations 0.1743366 4.249970 at 80iterations 9.7974584E-02 2.343381 at 90iterations 5.4987855E-02 1.341810 at 100iterations 3.0756732E-02 0.7856255 at 110iterations 1.7185753E-02 0.3814020 at 120iterations 9.6045202E-03 0.2330933 at 130iterations 5.3631933E-03 0.1149111 at 140iterations 2.9959562E-03 7.1076393E-02 at 150iterations 1.6712898E-03 3.6092758E-02 at 160iterations 9.3318196E-04 1.8795967E-02 at 170iterations 5.1997771E-04 1.0925293E-02 at 180iterations finished qdiffx linear iterations at : 10:31:28 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 5.1997771E-04 1.0925293E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 10:31:28 12.456u 0.198s 0:12.94 97.6% 0+0k 0+0io 0pf+0w