Sat Oct 8 16:32:06 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+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 Sat Oct 8 2011 at 16:32:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4503 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5447340 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): 21.30600 78.90300 ymin,ymax (A): 118.8860 184.2390 zmin,zma (A): -1.775000 59.81700 x,y,z range (A): 57.59700 65.35300 61.59200 scale (grids/A): 0.5447340 object centre (A): 50.10450 151.5625 29.02100 number of atom coordinates read : 4503 total number of charged atoms : 4333 net assigned charge : 5.000041 assigned positive charge : 690.7335 centred at (gu) : 90.74236 89.49226 87.41751 assigned negative charge : -685.7369 centred at (gu) : 90.74193 89.44217 87.46053 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8586 nv = 96 ne = 84 npr = 90785 no. pairs analyzed = 90785 no. exposed pairs = 5515 no. arc points = 38379 no. surface atoms = 1848 nbur = 2655 mkacc time = 0.1600000 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= 388 mr = 4587 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3000000 number of dielectric boundary points 4370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3885 ## 499 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 11403 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3378220E-09 -6.6296510E-11 midg,1,midg; midg,igrid,midg -2.3415173E-10 6.7644601E-10 1,midg,midg; igrid,midg,midg 2.3471952E-10 3.4518707E-10 gauss-seidel spectral radius is 0.9827380 estimated iterations to convergence 63 setup time was (sec) 0.4900000 now iterating at: 16:32:07 rms-change max change #iterations 9.0134673E-02 12.61209 at 10iterations 6.5693203E-03 0.9748611 at 20iterations 9.9171419E-04 0.1515522 at 30iterations 3.1151797E-04 4.7042847E-02 at 40iterations 1.0609729E-04 1.5239716E-02 at 50iterations finished qdiffx linear iterations at : 16:32:10 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 1.0609729E-04 1.5239716E-02 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 16:32:11 3.592u 0.206s 0:04.10 92.4% 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 Sat Oct 8 2011 at 16:32:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4503 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.634202 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): 21.30600 78.90300 ymin,ymax (A): 118.8860 184.2390 zmin,zma (A): -1.775000 59.81700 x,y,z range (A): 57.59700 65.35300 61.59200 scale (grids/A): 1.634202 object centre (A): 50.10450 151.5625 29.02100 number of atom coordinates read : 4503 total number of charged atoms : 4333 net assigned charge : 5.000041 assigned positive charge : 690.7335 centred at (gu) : 92.22637 88.47566 82.25124 assigned negative charge : -685.7369 centred at (gu) : 92.22553 88.32631 82.38110 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 96627 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38379 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 30524 mr = 67459 m= 3467 mr = 20917 m= 117 mr = 1777 m= 0 mr = 11 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1575 time to turn everything in is 0.4700000 number of dielectric boundary points 40571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 464 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 33163 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) : 0.5447340 object centre at (A) : 50.10450 151.5625 29.02100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4533173E-03 8.6938245E-03 midg,1,midg; midg,igrid,midg 1.4613054E-02 3.3162586E-02 1,midg,midg; igrid,midg,midg -1.3798187E-02 -1.0467573E-02 gauss-seidel spectral radius is 0.9983394 estimated iterations to convergence 195 setup time was (sec) 0.7100000 now iterating at: 16:32:12 rms-change max change #iterations 4.273544 186.5647 at 10iterations 1.843416 57.83125 at 20iterations 0.7953129 25.77561 at 30iterations 0.3456782 10.68495 at 40iterations 0.1498795 4.456364 at 50iterations 6.5090246E-02 1.871498 at 60iterations 2.8213287E-02 0.8889217 at 70iterations 1.2317104E-02 0.3978214 at 80iterations 5.4068551E-03 0.1606865 at 90iterations 2.4278320E-03 7.2170258E-02 at 100iterations 1.1119919E-03 3.5827637E-02 at 110iterations 5.4011820E-04 1.7265320E-02 at 120iterations finished qdiffx linear iterations at : 16:32:19 total time elapsed so far: 8.510000 # loops : 120 mean,max change (kT/e) : 5.4011820E-04 1.7265320E-02 energy calculations done at 8.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.640000 DelPhi exited at 16:32:20 8.644u 0.244s 0:09.18 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 16:32:20 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 = 4503 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.451303 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): 21.30600 78.90300 ymin,ymax (A): 118.8860 184.2390 zmin,zma (A): -1.775000 59.81700 x,y,z range (A): 57.59700 65.35300 61.59200 scale (grids/A): 2.451303 object centre (A): 50.10450 151.5625 29.02100 number of atom coordinates read : 4503 total number of charged atoms : 4333 net assigned charge : 5.000041 assigned positive charge : 690.7335 centred at (gu) : 93.33906 87.71339 78.37656 assigned negative charge : -685.7369 centred at (gu) : 93.33820 87.48952 78.57166 start vw surface at 0.1100000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 224507 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38379 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 106337 mr = 165232 m= 31048 mr = 84216 m= 5589 mr = 23075 m= 485 mr = 3729 m= 13 mr = 254 m= 0 mr = 0 time to grow re-entrant surface = 0.6999999 no. cavity mid-points inaccessible to solvent = 5262 time to turn everything in is 1.220000 number of dielectric boundary points 91473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 34623 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) : 1.634202 object centre at (A) : 50.10450 151.5625 29.02100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3012599E-03 0.2006728 midg,1,midg; midg,igrid,midg 0.1895540 0.5912635 1,midg,midg; igrid,midg,midg -0.2203218 -0.1730325 gauss-seidel spectral radius is 0.9992179 estimated iterations to convergence 282 setup time was (sec) 1.510000 now iterating at: 16:32:22 rms-change max change #iterations 10.99836 362.8869 at 10iterations 6.390048 133.9442 at 20iterations 3.686866 73.76517 at 30iterations 2.118855 38.32379 at 40iterations 1.214567 26.93357 at 50iterations 0.6925207 13.75599 at 60iterations 0.3953749 6.975658 at 70iterations 0.2250399 4.060634 at 80iterations 0.1279177 2.175690 at 90iterations 7.2640397E-02 1.345359 at 100iterations 4.1173976E-02 0.7266226 at 110iterations 2.3393381E-02 0.4450226 at 120iterations 1.3248163E-02 0.2270660 at 130iterations 7.5168866E-03 0.1291122 at 140iterations 4.2746807E-03 7.7116251E-02 at 150iterations 2.4371874E-03 4.0836334E-02 at 160iterations 1.3944183E-03 2.5184631E-02 at 170iterations 8.0624147E-04 1.4827728E-02 at 180iterations finished qdiffx linear iterations at : 16:32:35 total time elapsed so far: 15.02000 # loops : 180 mean,max change (kT/e) : 8.0624147E-04 1.4827728E-02 energy calculations done at 15.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.16000 DelPhi exited at 16:32:36 15.157u 0.281s 0:15.71 98.2% 0+0k 0+0io 0pf+0w