Sat Oct 8 11:38:14 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 Sat Oct 8 2011 at 11:38:14 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3114 !!! WARNING: GLM 62 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5580550 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): 0.1220000 60.04400 ymin,ymax (A): -18.85700 32.94600 zmin,zma (A): -7.530000 56.26300 x,y,z range (A): 59.92200 51.80300 63.79300 scale (grids/A): 0.5580550 object centre (A): 30.08300 7.044499 24.36650 number of atom coordinates read : 3114 total number of charged atoms : 2950 net assigned charge : -6.593986 assigned positive charge : 457.0348 centred at (gu) : 91.24200 88.41441 88.37811 assigned negative charge : -463.6301 centred at (gu) : 91.20879 88.35565 88.28364 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6819 nv = 96 ne = 84 npr = 58617 no. pairs analyzed = 58617 no. exposed pairs = 4524 no. arc points = 33515 no. surface atoms = 1521 nbur = 1593 mkacc time = 0.1600000 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= 322 mr = 3147 m= 0 mr = 11 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3303 ## 393 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8492 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4435478E-09 2.4499949E-10 midg,1,midg; midg,igrid,midg -1.8441892E-09 -6.8270168E-12 1,midg,midg; igrid,midg,midg -7.2834050E-10 -3.5229797E-10 gauss-seidel spectral radius is 0.9834748 estimated iterations to convergence 64 setup time was (sec) 0.6700000 now iterating at: 11:38:15 rms-change max change #iterations 8.4944874E-02 15.96751 at 10iterations 5.9131789E-03 1.012020 at 20iterations 4.1832982E-04 7.1498871E-02 at 30iterations 3.1614003E-05 5.3577423E-03 at 40iterations 2.8795414E-06 4.9018860E-04 at 50iterations finished qdiffx linear iterations at : 11:38:19 total time elapsed so far: 4.690000 # loops : 50 mean,max change (kT/e) : 2.8795414E-06 4.9018860E-04 energy calculations done at 4.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.860000 DelPhi exited at 11:38:20 4.863u 0.398s 0:05.95 88.2% 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 Sat Oct 8 2011 at 11:38:20 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3114 !!! WARNING: GLM 62 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.674165 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): 0.1220000 60.04400 ymin,ymax (A): -18.85700 32.94600 zmin,zma (A): -7.530000 56.26300 x,y,z range (A): 59.92200 51.80300 63.79300 scale (grids/A): 1.674165 object centre (A): 30.08300 7.044499 24.36650 number of atom coordinates read : 3114 total number of charged atoms : 2950 net assigned charge : -6.593986 assigned positive charge : 457.0348 centred at (gu) : 93.72506 85.24224 85.13370 assigned negative charge : -463.6301 centred at (gu) : 93.62600 85.06679 84.85050 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33515 grid for indexing accessible points = 1.400000 m= 23442 mr = 46716 m= 2738 mr = 15441 m= 89 mr = 1297 m= 3 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 36861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 358 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 22760 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) : 0.5580550 object centre at (A) : 30.08300 7.044499 24.36650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2196564E-02 -5.2832365E-03 midg,1,midg; midg,igrid,midg -1.1418210E-02 -2.2843757E-03 1,midg,midg; igrid,midg,midg -1.1320880E-02 -1.1959820E-02 gauss-seidel spectral radius is 0.9983172 estimated iterations to convergence 194 setup time was (sec) 0.9700000 now iterating at: 11:38:21 rms-change max change #iterations 3.613777 155.4370 at 10iterations 1.543483 58.08754 at 20iterations 0.6660486 22.88477 at 30iterations 0.2850687 10.79951 at 40iterations 0.1223689 4.490980 at 50iterations 5.2667011E-02 1.833886 at 60iterations 2.2613240E-02 0.7828693 at 70iterations 9.6932696E-03 0.4528828 at 80iterations 4.1813771E-03 0.1446466 at 90iterations 1.8017875E-03 6.3897967E-02 at 100iterations 7.7446195E-04 2.7105331E-02 at 110iterations 3.3327163E-04 1.3542175E-02 at 120iterations finished qdiffx linear iterations at : 11:38:35 total time elapsed so far: 14.12000 # loops : 120 mean,max change (kT/e) : 3.3327163E-04 1.3542175E-02 energy calculations done at 14.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.30000 DelPhi exited at 11:38:35 14.304u 0.524s 0:15.18 97.6% 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 Sat Oct 8 2011 at 11:38:35 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3114 !!! WARNING: GLM 62 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.511247 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): 0.1220000 60.04400 ymin,ymax (A): -18.85700 32.94600 zmin,zma (A): -7.530000 56.26300 x,y,z range (A): 59.92200 51.80300 63.79300 scale (grids/A): 2.511247 object centre (A): 30.08300 7.044499 24.36650 number of atom coordinates read : 3114 total number of charged atoms : 2950 net assigned charge : -6.593986 assigned positive charge : 457.0348 centred at (gu) : 95.58727 82.86297 82.70023 assigned negative charge : -463.6301 centred at (gu) : 95.43905 82.60017 82.27572 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 171552 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33515 grid for indexing accessible points = 1.400000 m= 77960 mr = 115190 m= 24359 mr = 59471 m= 4349 mr = 17959 m= 373 mr = 2769 m= 19 mr = 174 m= 0 mr = 4 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 83045 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 23584 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) : 1.674165 object centre at (A) : 30.08300 7.044499 24.36650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9068922 -4.3562185E-03 midg,1,midg; midg,igrid,midg -0.1561762 -3.0819569E-02 1,midg,midg; igrid,midg,midg -0.1547121 -0.1993283 gauss-seidel spectral radius is 0.9991981 estimated iterations to convergence 279 setup time was (sec) 2.150000 now iterating at: 11:38:38 rms-change max change #iterations 9.314499 308.0284 at 10iterations 5.360241 133.0071 at 20iterations 3.066831 64.73306 at 30iterations 1.752076 35.88270 at 40iterations 0.9922089 20.04896 at 50iterations 0.5599205 12.36557 at 60iterations 0.3167310 6.310388 at 70iterations 0.1788071 3.311293 at 80iterations 0.1005345 1.911489 at 90iterations 5.6593489E-02 1.280432 at 100iterations 3.1753227E-02 0.6357963 at 110iterations 1.7824832E-02 0.3695827 at 120iterations 1.0029246E-02 0.2112637 at 130iterations 5.6227245E-03 0.1081409 at 140iterations 3.1533458E-03 5.9064865E-02 at 150iterations 1.7728740E-03 3.7033081E-02 at 160iterations 9.9415600E-04 1.8875122E-02 at 170iterations 5.5816688E-04 1.3000488E-02 at 180iterations finished qdiffx linear iterations at : 11:39:08 total time elapsed so far: 31.82000 # loops : 180 mean,max change (kT/e) : 5.5816688E-04 1.3000488E-02 energy calculations done at 31.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 32.00000 DelPhi exited at 11:39:09 32.007u 0.888s 0:33.36 98.5% 0+0k 0+0io 0pf+0w