Wed Feb 15 08:56:01 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_thinner.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 Wed Feb 15 2012 at 08:56:01 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= 0.1400000 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 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8211 nv = 96 ne = 84 npr = 77563 no. pairs analyzed = 77563 no. exposed pairs = 5133 no. arc points = 35043 no. surface atoms = 1734 nbur = 2164 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 = 1.540000 m= 413 mr = 4310 m= 3 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4292 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3504 ## 346 charges are in solution ## iepsmp to db, and charging done at 0.5800000 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 0.9837932 estimated iterations to convergence 65 setup time was (sec) 0.7100000 now iterating at: 08:56:02 rms-change max change #iterations 9.9795826E-02 16.06115 at 10iterations 7.3505961E-03 1.020439 at 20iterations 8.7282981E-04 0.1268730 at 30iterations 4.4154187E-04 4.9416304E-02 at 40iterations 2.7913830E-04 3.1314373E-02 at 50iterations finished qdiffx linear iterations at : 08:56:05 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 2.7913830E-04 3.1314373E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 08:56:06 3.583u 0.172s 0:05.28 71.0% 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 Wed Feb 15 2012 at 08:56:07 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 ! 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= 0.1300000 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 0.2300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 90627 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35043 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30987 mr = 62417 m= 4035 mr = 21447 m= 144 mr = 2137 m= 0 mr = 25 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 160 time to turn everything in is 0.7400000 number of dielectric boundary points 39767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 341 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8700000 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 -5.0678939E-02 -1.0565164E-02 midg,1,midg; midg,igrid,midg 2.4049345E-02 -1.8426644E-03 1,midg,midg; igrid,midg,midg 3.9907591E-03 2.5628738E-03 gauss-seidel spectral radius is 0.9983989 estimated iterations to convergence 198 setup time was (sec) 1.030000 now iterating at: 08:56:08 rms-change max change #iterations 4.221308 177.8041 at 10iterations 1.852496 67.88970 at 20iterations 0.8207657 24.55920 at 30iterations 0.3615482 11.94547 at 40iterations 0.1591568 5.320523 at 50iterations 7.0469454E-02 2.572380 at 60iterations 3.1331420E-02 1.054651 at 70iterations 1.3985504E-02 0.4206554 at 80iterations 6.4265020E-03 0.1931725 at 90iterations 3.2331378E-03 0.1007080 at 100iterations 1.9431669E-03 6.0248852E-02 at 110iterations 1.4176907E-03 3.8852692E-02 at 120iterations finished qdiffx linear iterations at : 08:56:15 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 1.4176907E-03 3.8852692E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 08:56:15 7.817u 0.185s 0:08.47 94.3% 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 Wed Feb 15 2012 at 08:56:15 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= 0.1000000 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 0.1900000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 210173 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35043 grid for indexing accessible points = 1.400000 m= 103254 mr = 152574 m= 33620 mr = 81815 m= 6714 mr = 25301 m= 619 mr = 4517 m= 12 mr = 308 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 594 time to turn everything in is 1.730000 number of dielectric boundary points 89877 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.890000 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 -0.7438152 -0.1729816 midg,1,midg; midg,igrid,midg 0.3215970 -6.3225470E-02 1,midg,midg; igrid,midg,midg 0.1102094 -4.3613669E-02 gauss-seidel spectral radius is 0.9992313 estimated iterations to convergence 285 setup time was (sec) 2.080000 now iterating at: 08:56:18 rms-change max change #iterations 10.98478 399.8809 at 10iterations 6.537776 179.1727 at 20iterations 3.839432 80.94826 at 30iterations 2.237777 46.83578 at 40iterations 1.301297 27.76887 at 50iterations 0.7528249 14.93405 at 60iterations 0.4340415 7.953492 at 70iterations 0.2503160 5.488314 at 80iterations 0.1437622 2.519037 at 90iterations 8.2322970E-02 1.636536 at 100iterations 4.7277357E-02 0.8894424 at 110iterations 2.7074752E-02 0.4598961 at 120iterations 1.5526033E-02 0.2797757 at 130iterations 8.9468407E-03 0.1773453 at 140iterations 5.1836865E-03 9.7092628E-02 at 150iterations 3.0591404E-03 5.5648804E-02 at 160iterations 1.8857283E-03 3.4488678E-02 at 170iterations 1.2461778E-03 2.2894621E-02 at 180iterations finished qdiffx linear iterations at : 08:56:30 total time elapsed so far: 14.50000 # loops : 180 mean,max change (kT/e) : 1.2461778E-03 2.2894621E-02 energy calculations done at 14.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.69000 DelPhi exited at 08:56:31 14.691u 0.280s 0:15.79 94.8% 0+0k 0+0io 0pf+0w