Sat Feb 4 09:29:19 PST 2012 #!/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 Feb 4 2012 at 09:29:28 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 ! Automatically converted by prot2crg.py # of charge parameter records: 942 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3898 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: 0.5628904 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): 3.496000 66.71301 ymin,ymax (A): 0.7010001 61.84400 zmin,zma (A): -0.7909999 62.45400 x,y,z range (A): 63.21701 61.14300 63.24500 scale (grids/A): 0.5628904 object centre (A): 35.10450 31.27250 30.83150 number of atom coordinates read : 3898 total number of charged atoms : 3745 net assigned charge : -0.4999697 assigned positive charge : 587.9258 centred at (gu) : 89.38917 88.24306 88.09155 assigned negative charge : -588.4286 centred at (gu) : 89.34609 88.35579 88.01785 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8264 nv = 96 ne = 84 npr = 76161 no. pairs analyzed = 76161 no. exposed pairs = 5147 no. arc points = 35305 no. surface atoms = 1734 nbur = 2164 mkacc time = 0.1300000 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= 415 mr = 4327 m= 3 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 4330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3496 ## 345 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 10562 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0211623E-09 7.0078543E-10 midg,1,midg; midg,igrid,midg 2.6704052E-09 -1.2439878E-09 1,midg,midg; igrid,midg,midg -8.8292496E-10 5.4004301E-10 gauss-seidel spectral radius is 0.9837955 estimated iterations to convergence 65 setup time was (sec) 0.4700000 now iterating at: 09:29:30 rms-change max change #iterations 9.9905565E-02 16.06748 at 10iterations 7.3690922E-03 1.079422 at 20iterations 9.1593084E-04 0.1220932 at 30iterations 4.7587563E-04 5.3995132E-02 at 40iterations 3.0137785E-04 3.3723831E-02 at 50iterations finished qdiffx linear iterations at : 09:29:33 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 3.0137785E-04 3.3723831E-02 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 09:29:33 3.523u 0.174s 0:05.45 67.7% 0+0k 0+0io 3pf+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 Feb 4 2012 at 09:29:34 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 ! Automatically converted by prot2crg.py # of charge parameter records: 942 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3898 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: 1.688671 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): 3.496000 66.71301 ymin,ymax (A): 0.7010001 61.84400 zmin,zma (A): -0.7909999 62.45400 x,y,z range (A): 63.21701 61.14300 63.24500 scale (grids/A): 1.688671 object centre (A): 35.10450 31.27250 30.83150 number of atom coordinates read : 3898 total number of charged atoms : 3745 net assigned charge : -0.4999697 assigned positive charge : 587.9258 centred at (gu) : 88.16618 84.72784 84.27352 assigned negative charge : -588.4286 centred at (gu) : 88.03783 85.06686 84.05296 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 91319 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35305 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 31061 mr = 62903 m= 4046 mr = 21422 m= 140 mr = 2106 m= 0 mr = 23 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 160 time to turn everything in is 0.4500000 number of dielectric boundary points 40112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 340 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 28908 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) : 0.5628904 object centre at (A) : 35.10450 31.27250 30.83150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0716575E-02 -1.0506345E-02 midg,1,midg; midg,igrid,midg 2.4020365E-02 -1.7606607E-03 1,midg,midg; igrid,midg,midg 3.9774831E-03 2.5027688E-03 gauss-seidel spectral radius is 0.9984034 estimated iterations to convergence 199 setup time was (sec) 0.6700000 now iterating at: 09:29:36 rms-change max change #iterations 4.227180 177.5343 at 10iterations 1.857142 68.04077 at 20iterations 0.8238826 25.03172 at 30iterations 0.3629844 12.57341 at 40iterations 0.1600087 6.193878 at 50iterations 7.0914254E-02 2.148029 at 60iterations 3.1625979E-02 0.9884281 at 70iterations 1.4140503E-02 0.4398069 at 80iterations 6.5159397E-03 0.1932411 at 90iterations 3.2983716E-03 0.1047192 at 100iterations 1.9973768E-03 6.5846264E-02 at 110iterations 1.4632385E-03 3.9647102E-02 at 120iterations finished qdiffx linear iterations at : 09:29:43 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 1.4632385E-03 3.9647102E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 09:29:44 7.977u 0.209s 0:09.73 83.9% 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 Sat Feb 4 2012 at 09:29:44 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 ! Automatically converted by prot2crg.py # of charge parameter records: 942 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3898 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: 2.533006 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): 3.496000 66.71301 ymin,ymax (A): 0.7010001 61.84400 zmin,zma (A): -0.7909999 62.45400 x,y,z range (A): 63.21701 61.14300 63.24500 scale (grids/A): 2.533006 object centre (A): 35.10450 31.27250 30.83150 number of atom coordinates read : 3898 total number of charged atoms : 3745 net assigned charge : -0.4999697 assigned positive charge : 587.9258 centred at (gu) : 87.24892 82.09141 81.40997 assigned negative charge : -588.4286 centred at (gu) : 87.05669 82.60018 81.07946 start vw surface at 0.1300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 211814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35305 grid for indexing accessible points = 1.400000 m= 103675 mr = 153735 m= 33558 mr = 82032 m= 6697 mr = 25161 m= 613 mr = 4460 m= 12 mr = 299 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 594 time to turn everything in is 1.160000 number of dielectric boundary points 90682 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 29943 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) : 1.688671 object centre at (A) : 35.10450 31.27250 30.83150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7440572 -0.1728500 midg,1,midg; midg,igrid,midg 0.3212634 -6.4188503E-02 1,midg,midg; igrid,midg,midg 0.1099705 -4.3719575E-02 gauss-seidel spectral radius is 0.9992353 estimated iterations to convergence 285 setup time was (sec) 1.430000 now iterating at: 09:29:47 rms-change max change #iterations 10.98397 400.4368 at 10iterations 6.545065 179.6642 at 20iterations 3.848079 80.56774 at 30iterations 2.248260 47.02856 at 40iterations 1.309266 26.30382 at 50iterations 0.7583174 15.06361 at 60iterations 0.4378782 8.258110 at 70iterations 0.2528128 5.835565 at 80iterations 0.1452520 2.638035 at 90iterations 8.3409280E-02 1.555777 at 100iterations 4.7949981E-02 0.8806906 at 110iterations 2.7507169E-02 0.4960890 at 120iterations 1.5800247E-02 0.3051758 at 130iterations 9.1198096E-03 0.1746998 at 140iterations 5.2879304E-03 9.5680237E-02 at 150iterations 3.1270350E-03 5.8090210E-02 at 160iterations 1.9340415E-03 3.5254806E-02 at 170iterations 1.2833101E-03 2.5417328E-02 at 180iterations finished qdiffx linear iterations at : 09:29:59 total time elapsed so far: 13.23000 # loops : 180 mean,max change (kT/e) : 1.2833101E-03 2.5417328E-02 energy calculations done at 13.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.37000 DelPhi exited at 09:29:59 13.374u 0.210s 0:15.23 89.1% 0+0k 0+0io 0pf+0w