Sun Oct 9 04:28:40 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 04:28:40 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2713 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: 0.5396392 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): 41.41400 80.20500 ymin,ymax (A): 48.58500 114.5550 zmin,zma (A): -20.23700 37.00200 x,y,z range (A): 38.79100 65.97000 57.23900 scale (grids/A): 0.5396392 object centre (A): 60.80950 81.57000 8.382502 number of atom coordinates read : 2713 total number of charged atoms : 2579 net assigned charge : 4.000008 assigned positive charge : 386.5446 centred at (gu) : 90.88338 89.68340 90.85542 assigned negative charge : -382.5456 centred at (gu) : 90.94064 89.61444 90.90320 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5354 nv = 96 ne = 84 npr = 51898 no. pairs analyzed = 51898 no. exposed pairs = 4084 no. arc points = 28228 no. surface atoms = 1363 nbur = 1350 mkacc time = 0.1500000 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 = 1.568000 m= 267 mr = 2419 m= 3 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2715 ## 313 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 6846 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3390793E-10 -2.2942429E-11 midg,1,midg; midg,igrid,midg -1.2331976E-10 4.6797938E-10 1,midg,midg; igrid,midg,midg 3.6519887E-10 -7.7275818E-11 gauss-seidel spectral radius is 0.9822955 estimated iterations to convergence 62 setup time was (sec) 0.6400000 now iterating at: 04:28:41 rms-change max change #iterations 6.3907184E-02 10.63144 at 10iterations 4.6305098E-03 0.9013367 at 20iterations 1.3148100E-03 0.1507893 at 30iterations 7.1392761E-04 8.2088470E-02 at 40iterations 3.9660293E-04 4.5610428E-02 at 50iterations finished qdiffx linear iterations at : 04:28:45 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 3.9660293E-04 4.5610428E-02 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 04:28:45 4.350u 0.310s 0:04.93 94.5% 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 04:28:45 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2713 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: 1.618918 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): 41.41400 80.20500 ymin,ymax (A): 48.58500 114.5550 zmin,zma (A): -20.23700 37.00200 x,y,z range (A): 38.79100 65.97000 57.23900 scale (grids/A): 1.618918 object centre (A): 60.80950 81.57000 8.382502 number of atom coordinates read : 2713 total number of charged atoms : 2579 net assigned charge : 4.000008 assigned positive charge : 386.5446 centred at (gu) : 92.64953 89.04958 92.56558 assigned negative charge : -382.5456 centred at (gu) : 92.82150 88.84320 92.70954 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 58853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28228 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18283 mr = 37120 m= 2085 mr = 11495 m= 77 mr = 926 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 29752 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 231 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19739 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) : 0.5396392 object centre at (A) : 60.80950 81.57000 8.382502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1176964E-02 6.6765598E-03 midg,1,midg; midg,igrid,midg -1.5013662E-02 6.2669902E-03 1,midg,midg; igrid,midg,midg 5.8445302E-03 -1.1585715E-03 gauss-seidel spectral radius is 0.9981520 estimated iterations to convergence 185 setup time was (sec) 0.9100000 now iterating at: 04:28:47 rms-change max change #iterations 3.014897 150.6631 at 10iterations 1.251221 53.50875 at 20iterations 0.5230936 21.28752 at 30iterations 0.2179367 8.706024 at 40iterations 9.0264343E-02 3.398845 at 50iterations 3.7530150E-02 1.419317 at 60iterations 1.5837731E-02 0.5877094 at 70iterations 6.8967193E-03 0.3060846 at 80iterations 3.2911177E-03 0.1257057 at 90iterations 1.8825668E-03 6.7205191E-02 at 100iterations 1.3166638E-03 3.7643433E-02 at 110iterations 1.0194511E-03 2.5676727E-02 at 120iterations finished qdiffx linear iterations at : 04:28:56 total time elapsed so far: 9.810000 # loops : 120 mean,max change (kT/e) : 1.0194511E-03 2.5676727E-02 energy calculations done at 9.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.990000 DelPhi exited at 04:28:56 9.992u 0.335s 0:10.78 95.7% 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 04:28:56 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2713 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: 2.428376 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): 41.41400 80.20500 ymin,ymax (A): 48.58500 114.5550 zmin,zma (A): -20.23700 37.00200 x,y,z range (A): 38.79100 65.97000 57.23900 scale (grids/A): 2.428376 object centre (A): 60.80950 81.57000 8.382502 number of atom coordinates read : 2713 total number of charged atoms : 2579 net assigned charge : 4.000008 assigned positive charge : 386.5446 centred at (gu) : 93.97417 88.57410 93.84827 assigned negative charge : -382.5456 centred at (gu) : 94.23235 88.26487 94.06415 start vw surface at 0.1800000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 136414 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28228 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 61369 mr = 91899 m= 18527 mr = 45615 m= 3233 mr = 13073 m= 242 mr = 1985 m= 8 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 67124 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 20596 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) : 1.618918 object centre at (A) : 60.80950 81.57000 8.382502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3693553 0.1494815 midg,1,midg; midg,igrid,midg -0.2903223 0.1340594 1,midg,midg; igrid,midg,midg 9.3705148E-02 -2.9292699E-02 gauss-seidel spectral radius is 0.9991413 estimated iterations to convergence 270 setup time was (sec) 1.590000 now iterating at: 04:28:58 rms-change max change #iterations 8.167050 274.5707 at 10iterations 4.704324 131.6133 at 20iterations 2.689412 84.45206 at 30iterations 1.524693 36.67746 at 40iterations 0.8626432 24.22579 at 50iterations 0.4844678 11.70617 at 60iterations 0.2721479 6.722567 at 70iterations 0.1519040 3.609688 at 80iterations 8.4888458E-02 2.025299 at 90iterations 4.7351222E-02 1.122200 at 100iterations 2.6373029E-02 0.5785255 at 110iterations 1.4658416E-02 0.3426952 at 120iterations 8.1580859E-03 0.1930237 at 130iterations 4.5254859E-03 0.1024017 at 140iterations 2.5262581E-03 5.7443619E-02 at 150iterations 1.4235603E-03 3.9299011E-02 at 160iterations 8.1446400E-04 1.8084526E-02 at 170iterations 4.8832444E-04 1.1039734E-02 at 180iterations finished qdiffx linear iterations at : 04:29:12 total time elapsed so far: 15.70000 # loops : 180 mean,max change (kT/e) : 4.8832444E-04 1.1039734E-02 energy calculations done at 15.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.86000 DelPhi exited at 04:29:13 15.863u 0.360s 0:16.48 98.4% 0+0k 0+0io 0pf+0w