Sun Oct 9 01:48:50 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 Sun Oct 9 2011 at 01:48:50 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 = 3275 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5546812 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): -47.06100 7.337000 ymin,ymax (A): 175.8320 236.1300 zmin,zma (A): 78.97900 143.1600 x,y,z range (A): 54.39800 60.29799 64.18101 scale (grids/A): 0.5546812 object centre (A): -19.86200 205.9810 111.0695 number of atom coordinates read : 3275 total number of charged atoms : 3132 net assigned charge : 11.00004 assigned positive charge : 482.4366 centred at (gu) : 89.80548 90.23510 90.34920 assigned negative charge : -471.4383 centred at (gu) : 89.66434 90.16921 90.50208 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6819 nv = 96 ne = 84 npr = 62664 no. pairs analyzed = 62664 no. exposed pairs = 4584 no. arc points = 32491 no. surface atoms = 1505 nbur = 1770 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= 305 mr = 3330 m= 0 mr = 9 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3400000 number of dielectric boundary points 3785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3256 ## 409 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8783 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2278357E-09 -5.9956212E-10 midg,1,midg; midg,igrid,midg 3.0697370E-10 1.6963734E-09 1,midg,midg; igrid,midg,midg -4.5075377E-10 2.2082025E-09 gauss-seidel spectral radius is 0.9832762 estimated iterations to convergence 64 setup time was (sec) 0.5600000 now iterating at: 01:48:51 rms-change max change #iterations 8.2757697E-02 12.66722 at 10iterations 5.7489322E-03 0.8946080 at 20iterations 4.0252254E-04 6.3188553E-02 at 30iterations 3.1655833E-05 4.2746067E-03 at 40iterations 3.6987728E-06 7.0095062E-04 at 50iterations finished qdiffx linear iterations at : 01:48:53 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 3.6987728E-06 7.0095062E-04 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 01:48:54 3.132u 0.138s 0:03.57 91.3% 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 Sun Oct 9 2011 at 01:48:54 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 = 3275 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: 1.664044 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): -47.06100 7.337000 ymin,ymax (A): 175.8320 236.1300 zmin,zma (A): 78.97900 143.1600 x,y,z range (A): 54.39800 60.29799 64.18101 scale (grids/A): 1.664044 object centre (A): -19.86200 205.9810 111.0695 number of atom coordinates read : 3275 total number of charged atoms : 3132 net assigned charge : 11.00004 assigned positive charge : 482.4366 centred at (gu) : 89.41566 90.70419 91.04651 assigned negative charge : -471.4383 centred at (gu) : 88.99276 90.50733 91.50601 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75239 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32491 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23260 mr = 49230 m= 2536 mr = 15352 m= 90 mr = 1310 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1612 time to turn everything in is 0.5300000 number of dielectric boundary points 35230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 335 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 24100 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) : 0.5546812 object centre at (A) : -19.86200 205.9810 111.0695 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2361177E-03 -1.0540236E-02 midg,1,midg; midg,igrid,midg 1.0567618E-02 2.8030159E-02 1,midg,midg; igrid,midg,midg -2.7370241E-03 1.4884196E-02 gauss-seidel spectral radius is 0.9983084 estimated iterations to convergence 193 setup time was (sec) 0.8000000 now iterating at: 01:48:54 rms-change max change #iterations 3.573607 170.8057 at 10iterations 1.522460 52.25007 at 20iterations 0.6531195 22.71754 at 30iterations 0.2801528 9.778629 at 40iterations 0.1204400 4.261401 at 50iterations 5.1489331E-02 1.632967 at 60iterations 2.2003375E-02 0.7932363 at 70iterations 9.4896844E-03 0.3091707 at 80iterations 4.0506930E-03 0.1323633 at 90iterations 1.7372310E-03 6.4945936E-02 at 100iterations 7.4924133E-04 2.6753902E-02 at 110iterations 3.2227047E-04 1.0807037E-02 at 120iterations finished qdiffx linear iterations at : 01:49:00 total time elapsed so far: 6.760000 # loops : 120 mean,max change (kT/e) : 3.2227047E-04 1.0807037E-02 energy calculations done at 6.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.930000 DelPhi exited at 01:49:01 6.933u 0.157s 0:07.36 96.1% 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 Sun Oct 9 2011 at 01:49:01 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3275 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: 2.496066 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): -47.06100 7.337000 ymin,ymax (A): 175.8320 236.1300 zmin,zma (A): 78.97900 143.1600 x,y,z range (A): 54.39800 60.29799 64.18101 scale (grids/A): 2.496066 object centre (A): -19.86200 205.9810 111.0695 number of atom coordinates read : 3275 total number of charged atoms : 3132 net assigned charge : 11.00004 assigned positive charge : 482.4366 centred at (gu) : 89.12342 91.05617 91.56954 assigned negative charge : -471.4383 centred at (gu) : 88.48893 90.76094 92.25884 start vw surface at 0.1700000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 174402 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32491 grid for indexing accessible points = 1.400000 m= 79536 mr = 121029 m= 23105 mr = 61230 m= 4017 mr = 16928 m= 360 mr = 2687 m= 6 mr = 140 m= 3 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 5607 time to turn everything in is 1.220000 number of dielectric boundary points 79414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 25049 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) : 1.664044 object centre at (A) : -19.86200 205.9810 111.0695 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2754031 -9.3175501E-02 midg,1,midg; midg,igrid,midg 0.1832522 0.4568527 1,midg,midg; igrid,midg,midg -7.3153257E-02 0.1421518 gauss-seidel spectral radius is 0.9991952 estimated iterations to convergence 278 setup time was (sec) 1.510000 now iterating at: 01:49:03 rms-change max change #iterations 9.258882 331.4144 at 10iterations 5.361032 125.5543 at 20iterations 3.063169 65.41663 at 30iterations 1.747191 35.64348 at 40iterations 0.9896165 20.41393 at 50iterations 0.5623261 10.60383 at 60iterations 0.3171944 6.207551 at 70iterations 0.1789584 3.668702 at 80iterations 0.1008415 2.021455 at 90iterations 5.6676611E-02 1.094465 at 100iterations 3.1891540E-02 0.6710711 at 110iterations 1.7901814E-02 0.3476131 at 120iterations 1.0059779E-02 0.1946793 at 130iterations 5.6467182E-03 0.1100273 at 140iterations 3.1673873E-03 6.3125610E-02 at 150iterations 1.7746212E-03 3.6132813E-02 at 160iterations 9.9627685E-04 1.9218445E-02 at 170iterations 5.5972720E-04 1.0589600E-02 at 180iterations finished qdiffx linear iterations at : 01:49:12 total time elapsed so far: 10.92000 # loops : 180 mean,max change (kT/e) : 5.5972720E-04 1.0589600E-02 energy calculations done at 10.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.10000 DelPhi exited at 01:49:13 11.107u 0.181s 0:11.59 97.3% 0+0k 0+0io 0pf+0w