Sun Oct 9 14:59:52 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 Sun Oct 9 2011 at 14:59:52 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1424 !!! WARNING: HIR 87 has a net charge of 0.5140 !!! WARNING: GLU 107 has a net charge of -2.0000 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: 0.7295979 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): -6.391000 33.97100 ymin,ymax (A): -61.10900 -12.83800 zmin,zma (A): -29.42000 19.37400 x,y,z range (A): 40.36200 48.27100 48.79400 scale (grids/A): 0.7295979 object centre (A): 13.79000 -36.97350 -5.023000 number of atom coordinates read : 1424 total number of charged atoms : 1295 net assigned charge : 1.514008 assigned positive charge : 206.7964 centred at (gu) : 89.90504 91.24519 89.40594 assigned negative charge : -205.2823 centred at (gu) : 90.04770 91.13798 89.47468 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5376 nv = 96 ne = 84 npr = 28046 no. pairs analyzed = 28046 no. exposed pairs = 2069 no. arc points = 14421 no. surface atoms = 687 nbur = 737 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 367 mr = 2678 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.2300000 number of dielectric boundary points 3035 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1146 ## 78 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 5429 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2755923E-08 -1.4227300E-08 midg,1,midg; midg,igrid,midg -2.8574473E-08 9.6448034E-08 1,midg,midg; igrid,midg,midg 9.5775448E-08 -5.4674508E-08 gauss-seidel spectral radius is 0.9901506 estimated iterations to convergence 82 setup time was (sec) 0.4600000 now iterating at: 14:59:53 rms-change max change #iterations 0.1862470 36.29850 at 10iterations 2.3331851E-02 3.592176 at 20iterations 3.0495082E-03 0.4801412 at 30iterations 3.9372774E-04 7.3272705E-02 at 40iterations 4.9788323E-05 7.3623657E-03 at 50iterations finished qdiffx linear iterations at : 14:59:56 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 4.9788323E-05 7.3623657E-03 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 14:59:56 3.267u 0.146s 0:03.80 89.4% 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 14:59:56 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1424 !!! WARNING: HIR 87 has a net charge of 0.5140 !!! WARNING: GLU 107 has a net charge of -2.0000 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: 2.188794 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): -6.391000 33.97100 ymin,ymax (A): -61.10900 -12.83800 zmin,zma (A): -29.42000 19.37400 x,y,z range (A): 40.36200 48.27100 48.79400 scale (grids/A): 2.188794 object centre (A): 13.79000 -36.97350 -5.023000 number of atom coordinates read : 1424 total number of charged atoms : 1295 net assigned charge : 1.514008 assigned positive charge : 206.7964 centred at (gu) : 89.71539 93.73585 88.21808 assigned negative charge : -205.2823 centred at (gu) : 90.14338 93.41397 88.42417 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 56077 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14421 grid for indexing accessible points = 1.400000 m= 21722 mr = 36358 m= 4123 mr = 15518 m= 366 mr = 2506 m= 14 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1200 time to turn everything in is 0.4900000 number of dielectric boundary points 27808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 10310 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) : 0.7295979 object centre at (A) : 13.79000 -36.97350 -5.023000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3296302E-02 1.6933195E-02 midg,1,midg; midg,igrid,midg -7.8456569E-03 2.7048720E-02 1,midg,midg; igrid,midg,midg 1.8245345E-02 -4.2150738E-03 gauss-seidel spectral radius is 0.9988459 estimated iterations to convergence 233 setup time was (sec) 0.7600000 now iterating at: 14:59:57 rms-change max change #iterations 3.929899 190.5229 at 10iterations 1.957608 77.48696 at 20iterations 0.9731689 35.77645 at 30iterations 0.4860504 17.30866 at 40iterations 0.2418165 8.715251 at 50iterations 0.1200916 4.836997 at 60iterations 5.9892379E-02 1.993211 at 70iterations 2.9824356E-02 1.088023 at 80iterations 1.4828177E-02 0.4901886 at 90iterations 7.3534925E-03 0.2468262 at 100iterations 3.6486357E-03 0.1233158 at 110iterations 1.8200743E-03 6.1267853E-02 at 120iterations finished qdiffx linear iterations at : 15:00:04 total time elapsed so far: 7.120000 # loops : 120 mean,max change (kT/e) : 1.8200743E-03 6.1267853E-02 energy calculations done at 7.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.310000 DelPhi exited at 15:00:04 7.313u 0.161s 0:07.75 96.3% 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 15:00:04 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1424 !!! WARNING: HIR 87 has a net charge of 0.5140 !!! WARNING: GLU 107 has a net charge of -2.0000 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: 3.283191 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): -6.391000 33.97100 ymin,ymax (A): -61.10900 -12.83800 zmin,zma (A): -29.42000 19.37400 x,y,z range (A): 40.36200 48.27100 48.79400 scale (grids/A): 3.283191 object centre (A): 13.79000 -36.97350 -5.023000 number of atom coordinates read : 1424 total number of charged atoms : 1295 net assigned charge : 1.514008 assigned positive charge : 206.7964 centred at (gu) : 89.57316 95.60384 87.32732 assigned negative charge : -205.2823 centred at (gu) : 90.21506 95.12109 87.63637 start vw surface at 0.1300000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 128879 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14421 grid for indexing accessible points = 1.400000 m= 66596 mr = 87933 m= 27071 mr = 53389 m= 7382 mr = 21231 m= 1371 mr = 5352 m= 129 mr = 777 m= 7 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 4066 time to turn everything in is 1.410000 number of dielectric boundary points 62702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 10360 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) : 2.188794 object centre at (A) : 13.79000 -36.97350 -5.023000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7924609E-02 0.2982312 midg,1,midg; midg,igrid,midg -2.8647004E-02 4.3702055E-02 1,midg,midg; igrid,midg,midg 0.1411166 -4.2915262E-02 gauss-seidel spectral radius is 0.9993062 estimated iterations to convergence 300 setup time was (sec) 1.700000 now iterating at: 15:00:06 rms-change max change #iterations 8.830512 337.4272 at 10iterations 5.301413 221.0685 at 20iterations 3.153452 73.75409 at 30iterations 1.868033 45.63800 at 40iterations 1.104290 25.95807 at 50iterations 0.6530139 15.11614 at 60iterations 0.3837724 7.967081 at 70iterations 0.2257204 4.879412 at 80iterations 0.1326505 3.114319 at 90iterations 7.7592477E-02 1.515782 at 100iterations 4.5466505E-02 0.9628143 at 110iterations 2.6676159E-02 0.5873756 at 120iterations 1.5591484E-02 0.3169522 at 130iterations 9.0909498E-03 0.2103958 at 140iterations 5.3209797E-03 0.1112032 at 150iterations 3.1050516E-03 6.1529875E-02 at 160iterations 1.8137931E-03 3.5579681E-02 at 170iterations 1.0605791E-03 2.0592690E-02 at 180iterations finished qdiffx linear iterations at : 15:00:16 total time elapsed so far: 11.64000 # loops : 180 mean,max change (kT/e) : 1.0605791E-03 2.0592690E-02 energy calculations done at 11.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.82000 DelPhi exited at 15:00:16 11.823u 0.195s 0:12.29 97.7% 0+0k 0+0io 0pf+0w