Mon Oct 10 14:13:17 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 14:13:17 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2711 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: 0.5616736 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): -42.64800 10.78800 ymin,ymax (A): -7.097000 34.94600 zmin,zma (A): -42.24900 21.13300 x,y,z range (A): 53.43600 42.04300 63.38200 scale (grids/A): 0.5616736 object centre (A): -15.93000 13.92450 -10.55800 number of atom coordinates read : 2711 total number of charged atoms : 2576 net assigned charge : 1.0281801E-05 assigned positive charge : 396.9128 centred at (gu) : 90.04167 90.12042 91.23008 assigned negative charge : -396.9131 centred at (gu) : 90.10636 90.17968 91.40798 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5569 nv = 96 ne = 84 npr = 54940 no. pairs analyzed = 54940 no. exposed pairs = 3544 no. arc points = 25829 no. surface atoms = 1182 nbur = 1529 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 = 1.540000 m= 223 mr = 2734 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.3800000 number of dielectric boundary points 3055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2687 ## 364 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7303 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3738483E-09 -2.5445972E-09 midg,1,midg; midg,igrid,midg 6.2688110E-10 -6.1419608E-10 1,midg,midg; igrid,midg,midg 6.9461142E-10 -6.6082856E-10 gauss-seidel spectral radius is 0.9836317 estimated iterations to convergence 64 setup time was (sec) 0.6700000 now iterating at: 14:13:18 rms-change max change #iterations 8.1780247E-02 14.02343 at 10iterations 5.8378712E-03 0.8861856 at 20iterations 4.1460060E-04 7.8519821E-02 at 30iterations 2.9556035E-05 5.5398941E-03 at 40iterations 2.1343687E-06 3.2806396E-04 at 50iterations finished qdiffx linear iterations at : 14:13:21 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 2.1343687E-06 3.2806396E-04 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 14:13:22 4.198u 0.208s 0:04.87 90.1% 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 Mon Oct 10 2011 at 14:13:22 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2711 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.685021 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): -42.64800 10.78800 ymin,ymax (A): -7.097000 34.94600 zmin,zma (A): -42.24900 21.13300 x,y,z range (A): 53.43600 42.04300 63.38200 scale (grids/A): 1.685021 object centre (A): -15.93000 13.92450 -10.55800 number of atom coordinates read : 2711 total number of charged atoms : 2576 net assigned charge : 1.0281801E-05 assigned positive charge : 396.9128 centred at (gu) : 90.12424 90.36090 93.68951 assigned negative charge : -396.9131 centred at (gu) : 90.31869 90.53861 94.22348 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 61827 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25829 grid for indexing accessible points = 1.400000 m= 17895 mr = 40510 m= 1792 mr = 11699 m= 58 mr = 787 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2030 time to turn everything in is 0.5900000 number of dielectric boundary points 28576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 283 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 19906 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) : 0.5616736 object centre at (A) : -15.93000 13.92450 -10.55800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5705797E-02 -3.3852480E-02 midg,1,midg; midg,igrid,midg 3.4642117E-03 -8.4398984E-04 1,midg,midg; igrid,midg,midg 5.1754680E-03 -1.7687656E-02 gauss-seidel spectral radius is 0.9982654 estimated iterations to convergence 191 setup time was (sec) 0.9500000 now iterating at: 14:13:23 rms-change max change #iterations 3.341382 151.0535 at 10iterations 1.418242 54.98575 at 20iterations 0.6018490 23.12468 at 30iterations 0.2552128 9.418276 at 40iterations 0.1083293 3.900819 at 50iterations 4.6020441E-02 1.652265 at 60iterations 1.9488847E-02 0.6801491 at 70iterations 8.2789501E-03 0.3213921 at 80iterations 3.5130207E-03 0.1242561 at 90iterations 1.4943593E-03 5.8664322E-02 at 100iterations 6.3590374E-04 2.5234044E-02 at 110iterations 2.7024371E-04 1.0173321E-02 at 120iterations finished qdiffx linear iterations at : 14:13:31 total time elapsed so far: 9.070000 # loops : 120 mean,max change (kT/e) : 2.7024371E-04 1.0173321E-02 energy calculations done at 9.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.310000 DelPhi exited at 14:13:32 9.316u 0.216s 0:09.96 95.5% 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 14:13:32 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2711 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.527531 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): -42.64800 10.78800 ymin,ymax (A): -7.097000 34.94600 zmin,zma (A): -42.24900 21.13300 x,y,z range (A): 53.43600 42.04300 63.38200 scale (grids/A): 2.527531 object centre (A): -15.93000 13.92450 -10.55800 number of atom coordinates read : 2711 total number of charged atoms : 2576 net assigned charge : 1.0281801E-05 assigned positive charge : 396.9128 centred at (gu) : 90.18645 90.54126 95.53415 assigned negative charge : -396.9131 centred at (gu) : 90.47794 90.80787 96.33508 start vw surface at 0.2100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 143792 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25829 grid for indexing accessible points = 1.400000 m= 62546 mr = 99833 m= 16585 mr = 48137 m= 2767 mr = 11760 m= 207 mr = 1679 m= 6 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 6616 time to turn everything in is 1.370000 number of dielectric boundary points 64428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 20593 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) : 1.685021 object centre at (A) : -15.93000 13.92450 -10.55800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4061030 -0.5931670 midg,1,midg; midg,igrid,midg 3.6805246E-02 -2.8708450E-02 1,midg,midg; igrid,midg,midg 7.5572498E-02 -0.2822209 gauss-seidel spectral radius is 0.9991552 estimated iterations to convergence 272 setup time was (sec) 1.730000 now iterating at: 14:13:34 rms-change max change #iterations 8.439531 348.9185 at 10iterations 4.753037 114.5518 at 20iterations 2.649472 62.55191 at 30iterations 1.473527 36.00045 at 40iterations 0.8184981 17.67764 at 50iterations 0.4526677 11.58008 at 60iterations 0.2512784 5.352081 at 70iterations 0.1386606 3.023039 at 80iterations 7.6574333E-02 1.729743 at 90iterations 4.2421333E-02 1.016994 at 100iterations 2.3400795E-02 0.4669801 at 110iterations 1.2900786E-02 0.2747269 at 120iterations 7.1135429E-03 0.1614037 at 130iterations 3.9331964E-03 7.9773307E-02 at 140iterations 2.1700277E-03 4.5696259E-02 at 150iterations 1.1974809E-03 2.7378082E-02 at 160iterations 6.5954652E-04 1.3237000E-02 at 170iterations 3.6474806E-04 7.5216293E-03 at 180iterations finished qdiffx linear iterations at : 14:13:46 total time elapsed so far: 14.56000 # loops : 180 mean,max change (kT/e) : 3.6474806E-04 7.5216293E-03 energy calculations done at 14.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.79000 DelPhi exited at 14:13:47 14.792u 0.249s 0:15.47 97.1% 0+0k 0+0io 0pf+0w