Mon Oct 10 19:40:06 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 Mon Oct 10 2011 at 19:40:06 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 = 2566 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: 0.5652139 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): -24.91300 20.83600 ymin,ymax (A): -26.98800 22.52300 zmin,zma (A): -14.17500 48.81000 x,y,z range (A): 45.74900 49.51100 62.98500 scale (grids/A): 0.5652139 object centre (A): -2.038500 -2.232500 17.31750 number of atom coordinates read : 2566 total number of charged atoms : 2427 net assigned charge : 5.000030 assigned positive charge : 375.8809 centred at (gu) : 90.98569 90.98907 90.49473 assigned negative charge : -370.8819 centred at (gu) : 90.93076 91.01450 90.46179 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5213 nv = 96 ne = 84 npr = 52809 no. pairs analyzed = 52809 no. exposed pairs = 3458 no. arc points = 23684 no. surface atoms = 1162 nbur = 1404 mkacc time = 8.9999996E-02 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= 205 mr = 2558 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 2853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2413 ## 309 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6846 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4378871E-10 1.1262860E-09 midg,1,midg; midg,igrid,midg 7.2874595E-10 4.4304133E-10 1,midg,midg; igrid,midg,midg 2.5367392E-11 1.5736058E-09 gauss-seidel spectral radius is 0.9838177 estimated iterations to convergence 65 setup time was (sec) 0.3800000 now iterating at: 19:40:06 rms-change max change #iterations 7.8081489E-02 14.35958 at 10iterations 5.8300407E-03 0.9381781 at 20iterations 6.0763583E-04 0.1124983 at 30iterations 1.4659177E-04 2.9339790E-02 at 40iterations 4.7721191E-05 9.7084045E-03 at 50iterations finished qdiffx linear iterations at : 19:40:09 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 4.7721191E-05 9.7084045E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 19:40:10 3.446u 0.166s 0:04.10 87.8% 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 Mon Oct 10 2011 at 19:40:10 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 = 2566 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: 1.695642 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): -24.91300 20.83600 ymin,ymax (A): -26.98800 22.52300 zmin,zma (A): -14.17500 48.81000 x,y,z range (A): 45.74900 49.51100 62.98500 scale (grids/A): 1.695642 object centre (A): -2.038500 -2.232500 17.31750 number of atom coordinates read : 2566 total number of charged atoms : 2427 net assigned charge : 5.000030 assigned positive charge : 375.8809 centred at (gu) : 92.95635 92.96667 91.48371 assigned negative charge : -370.8819 centred at (gu) : 92.79211 93.04335 91.38527 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 56998 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23684 grid for indexing accessible points = 1.400000 m= 17455 mr = 37209 m= 2018 mr = 11756 m= 60 mr = 999 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 348 time to turn everything in is 0.2900000 number of dielectric boundary points 26557 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 225 iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 18753 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) : 0.5652139 object centre at (A) : -2.038500 -2.232500 17.31750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0918094E-03 -9.6663501E-04 midg,1,midg; midg,igrid,midg 3.9009997E-03 8.8960798E-03 1,midg,midg; igrid,midg,midg 9.6015520E-03 1.0957594E-02 gauss-seidel spectral radius is 0.9982765 estimated iterations to convergence 191 setup time was (sec) 0.5100000 now iterating at: 19:40:11 rms-change max change #iterations 3.253200 164.1084 at 10iterations 1.377557 54.04672 at 20iterations 0.5842955 25.62811 at 30iterations 0.2499700 9.702046 at 40iterations 0.1061714 3.955094 at 50iterations 4.5284003E-02 1.720633 at 60iterations 1.9288344E-02 0.7976990 at 70iterations 8.2597090E-03 0.3176551 at 80iterations 3.5506133E-03 0.1301415 at 90iterations 1.5563070E-03 6.2610626E-02 at 100iterations 7.0929952E-04 2.8287888E-02 at 110iterations 3.4505205E-04 1.4988899E-02 at 120iterations finished qdiffx linear iterations at : 19:40:18 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 3.4505205E-04 1.4988899E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 19:40:18 7.750u 0.199s 0:08.37 94.8% 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 Mon Oct 10 2011 at 19:40:18 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 = 2566 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: 2.543463 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): -24.91300 20.83600 ymin,ymax (A): -26.98800 22.52300 zmin,zma (A): -14.17500 48.81000 x,y,z range (A): 45.74900 49.51100 62.98500 scale (grids/A): 2.543463 object centre (A): -2.038500 -2.232500 17.31750 number of atom coordinates read : 2566 total number of charged atoms : 2427 net assigned charge : 5.000030 assigned positive charge : 375.8809 centred at (gu) : 94.43444 94.44990 92.22543 assigned negative charge : -370.8819 centred at (gu) : 94.18831 94.56496 92.07785 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 132289 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23684 grid for indexing accessible points = 1.400000 m= 58866 mr = 91381 m= 18055 mr = 45569 m= 3194 mr = 13500 m= 265 mr = 2094 m= 5 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1271 time to turn everything in is 0.7100000 number of dielectric boundary points 59995 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 19407 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) : 1.695642 object centre at (A) : -2.038500 -2.232500 17.31750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0443390E-03 0.1236252 midg,1,midg; midg,igrid,midg 5.2117083E-02 0.1742937 1,midg,midg; igrid,midg,midg 0.1419071 0.1353487 gauss-seidel spectral radius is 0.9991581 estimated iterations to convergence 272 setup time was (sec) 0.9300000 now iterating at: 19:40:20 rms-change max change #iterations 8.295659 285.1178 at 10iterations 4.709753 108.1288 at 20iterations 2.653234 64.39140 at 30iterations 1.492334 43.52008 at 40iterations 0.8345526 19.07600 at 50iterations 0.4671743 11.60585 at 60iterations 0.2600641 5.829388 at 70iterations 0.1450419 3.606391 at 80iterations 8.0583833E-02 2.163073 at 90iterations 4.4773739E-02 1.019269 at 100iterations 2.4847597E-02 0.5757084 at 110iterations 1.3793788E-02 0.3375721 at 120iterations 7.6680752E-03 0.1841431 at 130iterations 4.2567002E-03 9.3307495E-02 at 140iterations 2.3700627E-03 5.1513672E-02 at 150iterations 1.3296469E-03 2.9427528E-02 at 160iterations 7.5732823E-04 2.1005630E-02 at 170iterations 4.4115452E-04 1.0853291E-02 at 180iterations finished qdiffx linear iterations at : 19:40:31 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 4.4115452E-04 1.0853291E-02 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 19:40:31 12.074u 0.195s 0:12.54 97.7% 0+0k 0+0io 0pf+0w