Sat Oct 15 15:05:04 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+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 Oct 15 2011 at 15:05:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 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: 0.5483587 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): 4.584000 69.50500 ymin,ymax (A): 32.27000 94.31300 zmin,zma (A): 24.80300 79.50200 x,y,z range (A): 64.92101 62.04300 54.69900 scale (grids/A): 0.5483587 object centre (A): 37.04450 63.29150 52.15250 number of atom coordinates read : 3415 total number of charged atoms : 3274 net assigned charge : -6.499979 assigned positive charge : 513.8644 centred at (gu) : 87.84490 91.55009 88.11232 assigned negative charge : -520.3657 centred at (gu) : 87.79009 91.54054 88.13348 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6532 nv = 96 ne = 84 npr = 69633 no. pairs analyzed = 69633 no. exposed pairs = 4389 no. arc points = 30811 no. surface atoms = 1475 nbur = 1940 mkacc time = 0.1100000 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= 273 mr = 3295 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2400000 number of dielectric boundary points 3496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3139 ## 414 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8665 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9609704E-10 -3.8801679E-10 midg,1,midg; midg,igrid,midg -3.5389019E-10 -5.0952059E-10 1,midg,midg; igrid,midg,midg -1.5276495E-09 7.7516171E-12 gauss-seidel spectral radius is 0.9828843 estimated iterations to convergence 63 setup time was (sec) 0.4400000 now iterating at: 15:05:05 rms-change max change #iterations 8.0688156E-02 13.86095 at 10iterations 5.7762433E-03 0.9415092 at 20iterations 5.6875579E-04 9.2867851E-02 at 30iterations 1.1635341E-04 2.2753716E-02 at 40iterations 3.0279536E-05 5.9814453E-03 at 50iterations finished qdiffx linear iterations at : 15:05:10 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 3.0279536E-05 5.9814453E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 15:05:11 3.554u 0.185s 0:06.92 53.9% 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 Oct 15 2011 at 15:05:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 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: 1.645076 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): 4.584000 69.50500 ymin,ymax (A): 32.27000 94.31300 zmin,zma (A): 24.80300 79.50200 x,y,z range (A): 64.92101 62.04300 54.69900 scale (grids/A): 1.645076 object centre (A): 37.04450 63.29150 52.15250 number of atom coordinates read : 3415 total number of charged atoms : 3274 net assigned charge : -6.499979 assigned positive charge : 513.8644 centred at (gu) : 83.53378 94.64974 84.33613 assigned negative charge : -520.3657 centred at (gu) : 83.36996 94.62135 84.39986 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71615 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30811 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22854 mr = 47621 m= 2551 mr = 15708 m= 68 mr = 1276 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 2138 time to turn everything in is 0.3600000 number of dielectric boundary points 32483 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 384 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 25196 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) : 0.5483587 object centre at (A) : 37.04450 63.29150 52.15250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6530796E-03 -1.7363512E-03 midg,1,midg; midg,igrid,midg -4.0236907E-03 7.6468843E-03 1,midg,midg; igrid,midg,midg -2.0842856E-02 3.0236768E-02 gauss-seidel spectral radius is 0.9982480 estimated iterations to convergence 190 setup time was (sec) 0.5800000 now iterating at: 15:05:13 rms-change max change #iterations 3.642073 167.9873 at 10iterations 1.532800 60.70277 at 20iterations 0.6490088 24.46332 at 30iterations 0.2738066 10.60471 at 40iterations 0.1158030 3.871296 at 50iterations 4.9166750E-02 1.753459 at 60iterations 2.0896893E-02 0.6903780 at 70iterations 8.8711176E-03 0.3763313 at 80iterations 3.7931949E-03 0.1484742 at 90iterations 1.6402662E-03 5.3990364E-02 at 100iterations 7.2853302E-04 3.0727386E-02 at 110iterations 3.3588952E-04 1.4755249E-02 at 120iterations finished qdiffx linear iterations at : 15:05:27 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 3.3588952E-04 1.4755249E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 15:05:28 8.066u 0.235s 0:16.96 48.8% 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 Oct 15 2011 at 15:05:28 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 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: 2.467614 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): 4.584000 69.50500 ymin,ymax (A): 32.27000 94.31300 zmin,zma (A): 24.80300 79.50200 x,y,z range (A): 64.92101 62.04300 54.69900 scale (grids/A): 2.467614 object centre (A): 37.04450 63.29150 52.15250 number of atom coordinates read : 3415 total number of charged atoms : 3274 net assigned charge : -6.499979 assigned positive charge : 513.8644 centred at (gu) : 80.30032 96.97442 81.50404 assigned negative charge : -520.3657 centred at (gu) : 80.05463 96.93196 81.59962 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 166159 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30811 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 77398 mr = 116781 m= 23183 mr = 60854 m= 4041 mr = 17447 m= 248 mr = 2593 m= 3 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 7423 time to turn everything in is 0.9200000 number of dielectric boundary points 73274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 26157 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) : 1.645076 object centre at (A) : 37.04450 63.29150 52.15250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1130289E-02 -4.0546492E-02 midg,1,midg; midg,igrid,midg 5.6084383E-02 0.1637004 1,midg,midg; igrid,midg,midg -0.5231200 0.6069190 gauss-seidel spectral radius is 0.9991682 estimated iterations to convergence 274 setup time was (sec) 1.180000 now iterating at: 15:05:29 rms-change max change #iterations 9.409631 291.5420 at 10iterations 5.352280 134.5940 at 20iterations 3.031342 76.73828 at 30iterations 1.704067 40.87936 at 40iterations 0.9568112 23.00988 at 50iterations 0.5368962 13.10487 at 60iterations 0.2997846 6.520656 at 70iterations 0.1675431 4.475304 at 80iterations 9.3320504E-02 1.979490 at 90iterations 5.1957313E-02 1.137592 at 100iterations 2.9012235E-02 0.6508423 at 110iterations 1.6187159E-02 0.3318176 at 120iterations 9.0212589E-03 0.1736845 at 130iterations 5.0215181E-03 9.7540855E-02 at 140iterations 2.8136335E-03 5.3222656E-02 at 150iterations 1.5809626E-03 3.7643999E-02 at 160iterations 8.9709531E-04 1.9696236E-02 at 170iterations 5.1535643E-04 1.1070251E-02 at 180iterations finished qdiffx linear iterations at : 15:05:42 total time elapsed so far: 13.51000 # loops : 180 mean,max change (kT/e) : 5.1535643E-04 1.1070251E-02 energy calculations done at 13.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.65000 DelPhi exited at 15:05:42 13.647u 0.269s 0:14.25 97.5% 0+0k 0+0io 0pf+0w