Tue Oct 11 06:00:37 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 Tue Oct 11 2011 at 06:00:37 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.7156498 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): 25.86900 72.58200 ymin,ymax (A): -18.46200 31.28300 zmin,zma (A): 4.071000 46.48400 x,y,z range (A): 46.71300 49.74500 42.41300 scale (grids/A): 0.7156498 object centre (A): 49.22550 6.410501 25.27750 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 89.14558 90.16866 90.28115 assigned negative charge : -317.2741 centred at (gu) : 89.28548 90.11515 90.36342 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7294 nv = 96 ne = 84 npr = 42822 no. pairs analyzed = 42822 no. exposed pairs = 2558 no. arc points = 17462 no. surface atoms = 886 nbur = 1432 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 494 mr = 4209 m= 4 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3477 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1628 ## 150 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8115 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0896651E-07 1.6482595E-08 midg,1,midg; midg,igrid,midg 3.2415684E-08 1.0104613E-07 1,midg,midg; igrid,midg,midg 1.7570045E-07 -1.6063710E-08 gauss-seidel spectral radius is 0.9898217 estimated iterations to convergence 81 setup time was (sec) 0.5100000 now iterating at: 06:00:37 rms-change max change #iterations 0.2127127 33.37818 at 10iterations 2.7192306E-02 3.843004 at 20iterations 3.6594907E-03 0.4440002 at 30iterations 6.3687318E-04 8.5201263E-02 at 40iterations 1.7003587E-04 2.3309708E-02 at 50iterations finished qdiffx linear iterations at : 06:00:40 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 1.7003587E-04 2.3309708E-02 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 06:00:41 3.353u 0.179s 0:03.83 91.9% 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 Tue Oct 11 2011 at 06:00:41 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.146949 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): 25.86900 72.58200 ymin,ymax (A): -18.46200 31.28300 zmin,zma (A): 4.071000 46.48400 x,y,z range (A): 46.71300 49.74500 42.41300 scale (grids/A): 2.146949 object centre (A): 49.22550 6.410501 25.27750 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 87.43673 90.50588 90.84339 assigned negative charge : -317.2741 centred at (gu) : 87.85654 90.34549 91.09058 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77314 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17462 grid for indexing accessible points = 1.400000 m= 31773 mr = 55048 m= 6249 mr = 24295 m= 609 mr = 4247 m= 20 mr = 296 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 32079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15855 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) : 0.7156498 object centre at (A) : 49.22550 6.410501 25.27750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3954554E-02 3.4365982E-02 midg,1,midg; midg,igrid,midg 4.7450878E-02 2.9947726E-02 1,midg,midg; igrid,midg,midg 4.8241269E-02 -5.9017900E-02 gauss-seidel spectral radius is 0.9988557 estimated iterations to convergence 234 setup time was (sec) 0.9100000 now iterating at: 06:00:42 rms-change max change #iterations 4.728622 209.6771 at 10iterations 2.356137 81.66798 at 20iterations 1.180329 36.82243 at 30iterations 0.5889977 17.74506 at 40iterations 0.2953491 9.093326 at 50iterations 0.1470929 4.114583 at 60iterations 7.3792383E-02 2.150944 at 70iterations 3.7141863E-02 1.111898 at 80iterations 1.8595228E-02 0.5345154 at 90iterations 9.4153862E-03 0.2746391 at 100iterations 4.7715493E-03 0.1674194 at 110iterations 2.4863954E-03 7.7716827E-02 at 120iterations finished qdiffx linear iterations at : 06:00:48 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 2.4863954E-03 7.7716827E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 06:00:49 7.755u 0.212s 0:08.24 96.6% 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 Tue Oct 11 2011 at 06:00:49 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 3.220424 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): 25.86900 72.58200 ymin,ymax (A): -18.46200 31.28300 zmin,zma (A): 4.071000 46.48400 x,y,z range (A): 46.71300 49.74500 42.41300 scale (grids/A): 3.220424 object centre (A): 49.22550 6.410501 25.27750 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 86.15515 90.75894 91.26508 assigned negative charge : -317.2741 centred at (gu) : 86.78480 90.51832 91.63586 start vw surface at 0.1600000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 178337 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17462 grid for indexing accessible points = 1.400000 m= 98452 mr = 132765 m= 41107 mr = 82332 m= 11980 mr = 33977 m= 2452 mr = 9395 m= 291 mr = 1752 m= 14 mr = 169 m= 0 mr = 5 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.880000 number of dielectric boundary points 72238 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 15952 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) : 2.146949 object centre at (A) : 49.22550 6.410501 25.27750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1269897 0.2590740 midg,1,midg; midg,igrid,midg 0.4026728 0.1483271 1,midg,midg; igrid,midg,midg 0.4698489 -0.6830181 gauss-seidel spectral radius is 0.9993029 estimated iterations to convergence 299 setup time was (sec) 2.200000 now iterating at: 06:00:51 rms-change max change #iterations 10.45141 360.3873 at 10iterations 6.194112 144.8134 at 20iterations 3.677265 72.15837 at 30iterations 2.178247 45.05705 at 40iterations 1.284351 24.24099 at 50iterations 0.7556486 14.91543 at 60iterations 0.4456916 7.900556 at 70iterations 0.2622168 5.117886 at 80iterations 0.1542342 2.572109 at 90iterations 9.0701878E-02 1.559021 at 100iterations 5.3301293E-02 0.8770504 at 110iterations 3.1469911E-02 0.5079269 at 120iterations 1.8682711E-02 0.3180790 at 130iterations 1.1265262E-02 0.1994019 at 140iterations 6.9056321E-03 0.1256981 at 150iterations 4.3779439E-03 8.8172913E-02 at 160iterations 2.9278877E-03 5.6476593E-02 at 170iterations 2.0723070E-03 3.9155960E-02 at 180iterations finished qdiffx linear iterations at : 06:01:02 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 2.0723070E-03 3.9155960E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 06:01:02 12.921u 0.264s 0:13.50 97.6% 0+0k 0+0io 0pf+0w