Wed Dec 28 11:03:02 PST 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 Wed Dec 28 2011 at 11:03:02 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5787395 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): -25.66800 35.84500 ymin,ymax (A): -19.00900 20.51000 zmin,zma (A): -3.572000 38.47600 x,y,z range (A): 61.51300 39.51900 42.04800 scale (grids/A): 0.5787395 object centre (A): 5.088501 0.7505007 17.45200 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 267.4744 centred at (gu) : 89.89677 90.24464 90.58446 assigned negative charge : -289.4262 centred at (gu) : 89.89694 90.35088 90.73638 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4442 nv = 96 ne = 84 npr = 39977 no. pairs analyzed = 39977 no. exposed pairs = 2398 no. arc points = 17166 no. surface atoms = 810 nbur = 1154 mkacc time = 0.1000000 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 = 1.512000 m= 176 mr = 2440 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.2400000 number of dielectric boundary points 2170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1667 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 5346 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2198741E-09 -7.6697715E-09 midg,1,midg; midg,igrid,midg -2.9641287E-09 -6.4011036E-09 1,midg,midg; igrid,midg,midg -4.6772040E-09 -4.4676622E-09 gauss-seidel spectral radius is 0.9845072 estimated iterations to convergence 66 setup time was (sec) 0.6200000 now iterating at: 11:03:03 rms-change max change #iterations 8.2438938E-02 16.20028 at 10iterations 6.4009866E-03 1.167564 at 20iterations 4.9761281E-04 9.5954895E-02 at 30iterations 3.8556158E-05 8.2817078E-03 at 40iterations 2.9735072E-06 5.4204464E-04 at 50iterations finished qdiffx linear iterations at : 11:03:10 total time elapsed so far: 7.600000 # loops : 50 mean,max change (kT/e) : 2.9735072E-06 5.4204464E-04 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 11:03:11 7.768u 0.565s 0:08.93 93.1% 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 Wed Dec 28 2011 at 11:03:11 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.736218 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): -25.66800 35.84500 ymin,ymax (A): -19.00900 20.51000 zmin,zma (A): -3.572000 38.47600 x,y,z range (A): 61.51300 39.51900 42.04800 scale (grids/A): 1.736218 object centre (A): 5.088501 0.7505007 17.45200 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 267.4744 centred at (gu) : 89.69082 90.73429 91.75362 assigned negative charge : -289.4262 centred at (gu) : 89.69092 91.05296 92.20919 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 48572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17166 grid for indexing accessible points = 1.400000 m= 16339 mr = 33481 m= 1819 mr = 12239 m= 46 mr = 1038 m= 0 mr = 7 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2269 time to turn everything in is 0.4000000 number of dielectric boundary points 20011 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 13751 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) : 0.5787395 object centre at (A) : 5.088501 0.7505007 17.45200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5411224E-03 -2.7111115E-02 midg,1,midg; midg,igrid,midg -1.0670987E-02 -2.1636996E-02 1,midg,midg; igrid,midg,midg -2.2028003E-02 -2.9823286E-02 gauss-seidel spectral radius is 0.9982799 estimated iterations to convergence 191 setup time was (sec) 0.8100000 now iterating at: 11:03:12 rms-change max change #iterations 2.988300 149.5100 at 10iterations 1.270572 59.95849 at 20iterations 0.5446457 22.77932 at 30iterations 0.2318320 8.760437 at 40iterations 9.8938406E-02 4.613171 at 50iterations 4.2362042E-02 1.671082 at 60iterations 1.8040536E-02 0.7167940 at 70iterations 7.6681911E-03 0.3075085 at 80iterations 3.2733690E-03 0.1299477 at 90iterations 1.3971217E-03 5.4542542E-02 at 100iterations 5.9921527E-04 2.4184227E-02 at 110iterations 2.5450447E-04 1.0204315E-02 at 120iterations finished qdiffx linear iterations at : 11:03:29 total time elapsed so far: 17.72000 # loops : 120 mean,max change (kT/e) : 2.5450447E-04 1.0204315E-02 energy calculations done at 17.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.89000 DelPhi exited at 11:03:30 17.895u 0.618s 0:18.82 98.2% 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 Dec 28 2011 at 11:03:30 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.604327 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): -25.66800 35.84500 ymin,ymax (A): -19.00900 20.51000 zmin,zma (A): -3.572000 38.47600 x,y,z range (A): 61.51300 39.51900 42.04800 scale (grids/A): 2.604327 object centre (A): 5.088501 0.7505007 17.45200 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 267.4744 centred at (gu) : 89.53625 91.10141 92.63051 assigned negative charge : -289.4262 centred at (gu) : 89.53645 91.57946 93.31384 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 112334 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17166 grid for indexing accessible points = 1.400000 m= 55436 mr = 80754 m= 17221 mr = 45751 m= 2831 mr = 14093 m= 164 mr = 2037 m= 2 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 8289 time to turn everything in is 0.9900000 number of dielectric boundary points 45250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 14110 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) : 1.736218 object centre at (A) : 5.088501 0.7505007 17.45200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6979457E-02 -0.3210509 midg,1,midg; midg,igrid,midg -0.1231492 -0.2601461 1,midg,midg; igrid,midg,midg -0.2458076 -0.3530950 gauss-seidel spectral radius is 0.9991345 estimated iterations to convergence 269 setup time was (sec) 1.340000 now iterating at: 11:03:32 rms-change max change #iterations 7.299225 232.6147 at 10iterations 4.029341 113.7257 at 20iterations 2.213135 52.74635 at 30iterations 1.214637 32.03986 at 40iterations 0.6674151 15.13601 at 50iterations 0.3644302 8.521727 at 60iterations 0.2003353 4.525940 at 70iterations 0.1094763 2.446787 at 80iterations 5.9859790E-02 1.423422 at 90iterations 3.2757804E-02 0.7588501 at 100iterations 1.7918581E-02 0.5073175 at 110iterations 9.8133720E-03 0.2247524 at 120iterations 5.3765569E-03 0.1294632 at 130iterations 2.9331418E-03 6.4337254E-02 at 140iterations 1.6126835E-03 3.5309792E-02 at 150iterations 8.7926176E-04 2.0126343E-02 at 160iterations 4.8128696E-04 1.0566711E-02 at 170iterations 2.6374287E-04 6.0958862E-03 at 180iterations finished qdiffx linear iterations at : 11:03:59 total time elapsed so far: 28.89000 # loops : 180 mean,max change (kT/e) : 2.6374287E-04 6.0958862E-03 energy calculations done at 28.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.07000 DelPhi exited at 11:04:00 29.077u 0.620s 0:30.49 97.3% 0+0k 0+0io 0pf+0w