Tue Oct 11 03:19:57 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 Tue Oct 11 2011 at 03:19:58 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4486 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: SEP 227 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5459536 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): -2.767000 57.86000 ymin,ymax (A): -42.79100 22.41600 zmin,zma (A): -48.05300 16.47600 x,y,z range (A): 60.62700 65.20700 64.52900 scale (grids/A): 0.5459536 object centre (A): 27.54650 -10.18750 -15.78850 number of atom coordinates read : 4486 total number of charged atoms : 4332 net assigned charge : -6.568956 assigned positive charge : 679.1149 centred at (gu) : 90.05711 90.86757 91.57445 assigned negative charge : -685.6886 centred at (gu) : 90.05978 90.89097 91.56682 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8703 nv = 96 ne = 84 npr = 88587 no. pairs analyzed = 88587 no. exposed pairs = 5987 no. arc points = 42940 no. surface atoms = 1983 nbur = 2503 mkacc time = 0.1900000 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= 383 mr = 4348 m= 0 mr = 17 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.4500000 number of dielectric boundary points 4721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4393 ## 607 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 11548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3208908E-10 -4.7919380E-10 midg,1,midg; midg,igrid,midg -1.3882981E-10 -7.9937867E-10 1,midg,midg; igrid,midg,midg -3.7399203E-10 -4.3979606E-10 gauss-seidel spectral radius is 0.9828295 estimated iterations to convergence 63 setup time was (sec) 0.6900000 now iterating at: 03:19:58 rms-change max change #iterations 9.0523429E-02 12.61232 at 10iterations 6.1598518E-03 0.8567543 at 20iterations 4.6045354E-04 8.2372665E-02 at 30iterations 7.2230978E-05 1.3268352E-02 at 40iterations 2.0430043E-05 3.8182735E-03 at 50iterations finished qdiffx linear iterations at : 03:20:01 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 2.0430043E-05 3.8182735E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 03:20:02 3.583u 0.238s 0:04.18 91.1% 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 Oct 11 2011 at 03:20:02 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4486 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: SEP 227 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.637861 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): -2.767000 57.86000 ymin,ymax (A): -42.79100 22.41600 zmin,zma (A): -48.05300 16.47600 x,y,z range (A): 60.62700 65.20700 64.52900 scale (grids/A): 1.637861 object centre (A): 27.54650 -10.18750 -15.78850 number of atom coordinates read : 4486 total number of charged atoms : 4332 net assigned charge : -6.568956 assigned positive charge : 679.1149 centred at (gu) : 90.16989 92.60104 94.72169 assigned negative charge : -685.6886 centred at (gu) : 90.17889 92.67275 94.69985 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 96140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42940 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 29784 mr = 63597 m= 3233 mr = 19941 m= 91 mr = 1463 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 463 time to turn everything in is 0.6700000 number of dielectric boundary points 44240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 501 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 33074 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) : 0.5459536 object centre at (A) : 27.54650 -10.18750 -15.78850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9843485E-02 1.3860554E-02 midg,1,midg; midg,igrid,midg -1.2886684E-02 -1.2848066E-02 1,midg,midg; igrid,midg,midg -1.5968733E-02 -2.0222054E-03 gauss-seidel spectral radius is 0.9983729 estimated iterations to convergence 197 setup time was (sec) 0.9900000 now iterating at: 03:20:03 rms-change max change #iterations 4.300777 166.1027 at 10iterations 1.875533 73.84794 at 20iterations 0.8165446 28.34837 at 30iterations 0.3549122 10.56119 at 40iterations 0.1551768 4.591083 at 50iterations 6.7875616E-02 2.242302 at 60iterations 2.9615557E-02 0.8780060 at 70iterations 1.2959857E-02 0.4303398 at 80iterations 5.6645675E-03 0.1647949 at 90iterations 2.4824832E-03 8.3461761E-02 at 100iterations 1.0899088E-03 3.2062292E-02 at 110iterations 4.8150533E-04 1.5253365E-02 at 120iterations finished qdiffx linear iterations at : 03:20:10 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 4.8150533E-04 1.5253365E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 03:20:10 8.039u 0.257s 0:08.66 95.6% 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 Tue Oct 11 2011 at 03:20:10 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4486 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: SEP 227 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.456791 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): -2.767000 57.86000 ymin,ymax (A): -42.79100 22.41600 zmin,zma (A): -48.05300 16.47600 x,y,z range (A): 60.62700 65.20700 64.52900 scale (grids/A): 2.456791 object centre (A): 27.54650 -10.18750 -15.78850 number of atom coordinates read : 4486 total number of charged atoms : 4332 net assigned charge : -6.568956 assigned positive charge : 679.1149 centred at (gu) : 90.25454 93.90131 97.08218 assigned negative charge : -685.6886 centred at (gu) : 90.26819 94.00903 97.04967 start vw surface at 0.1900000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 223413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42940 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 102290 mr = 156509 m= 29713 mr = 79414 m= 4815 mr = 21764 m= 351 mr = 2944 m= 14 mr = 114 m= 0 mr = 2 time to grow re-entrant surface = 0.9400001 no. cavity mid-points inaccessible to solvent = 1608 time to turn everything in is 1.620000 number of dielectric boundary points 99849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 34612 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) : 1.637861 object centre at (A) : 27.54650 -10.18750 -15.78850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4418033 0.2681392 midg,1,midg; midg,igrid,midg -0.1141045 -0.2152317 1,midg,midg; igrid,midg,midg -0.2640934 4.9554225E-02 gauss-seidel spectral radius is 0.9992547 estimated iterations to convergence 289 setup time was (sec) 1.960000 now iterating at: 03:20:13 rms-change max change #iterations 11.28255 336.4651 at 10iterations 6.709422 140.0146 at 20iterations 3.967560 91.29205 at 30iterations 2.330693 47.47552 at 40iterations 1.363962 27.12394 at 50iterations 0.7934354 16.91713 at 60iterations 0.4605151 9.293549 at 70iterations 0.2681977 5.604921 at 80iterations 0.1550077 2.892190 at 90iterations 8.9565985E-02 1.804262 at 100iterations 5.1734459E-02 0.9687166 at 110iterations 2.9807150E-02 0.5373178 at 120iterations 1.7172396E-02 0.3175583 at 130iterations 9.8849032E-03 0.1720108 at 140iterations 5.6850431E-03 0.1014900 at 150iterations 3.2761707E-03 6.0207367E-02 at 160iterations 1.8792717E-03 3.6949396E-02 at 170iterations 1.0813707E-03 1.8131256E-02 at 180iterations finished qdiffx linear iterations at : 03:20:24 total time elapsed so far: 13.41000 # loops : 180 mean,max change (kT/e) : 1.0813707E-03 1.8131256E-02 energy calculations done at 13.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.58000 DelPhi exited at 03:20:25 13.579u 0.258s 0:14.27 96.8% 0+0k 0+0io 0pf+0w