Tue Oct 11 05:28:19 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 05:28:19 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 = 2246 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: 0.6926475 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): 19.81500 63.11300 ymin,ymax (A): -3.596000 34.76300 zmin,zma (A): 20.49100 71.88800 x,y,z range (A): 43.29800 38.35900 51.39700 scale (grids/A): 0.6926475 object centre (A): 41.46400 15.58350 46.18950 number of atom coordinates read : 2246 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 90.13641 89.30271 89.27431 assigned negative charge : -303.7472 centred at (gu) : 90.31792 89.32343 89.26592 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6766 nv = 96 ne = 84 npr = 40994 no. pairs analyzed = 40994 no. exposed pairs = 2506 no. arc points = 17107 no. surface atoms = 852 nbur = 1394 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 448 mr = 3913 m= 6 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1613 ## 118 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7479 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7686303E-08 4.1123929E-08 midg,1,midg; midg,igrid,midg 5.8942788E-08 3.2655837E-08 1,midg,midg; igrid,midg,midg 1.0276224E-07 -1.9741744E-08 gauss-seidel spectral radius is 0.9891382 estimated iterations to convergence 78 setup time was (sec) 0.5300000 now iterating at: 05:28:20 rms-change max change #iterations 0.1735834 24.77300 at 10iterations 2.0672288E-02 2.939884 at 20iterations 2.5972854E-03 0.4028969 at 30iterations 4.3280984E-04 5.5640221E-02 at 40iterations 1.0996708E-04 1.3183594E-02 at 50iterations finished qdiffx linear iterations at : 05:28:22 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.0996708E-04 1.3183594E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 05:28:23 3.344u 0.148s 0:03.83 90.8% 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 Tue Oct 11 2011 at 05:28:23 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 = 2246 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: 2.077942 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): 19.81500 63.11300 ymin,ymax (A): -3.596000 34.76300 zmin,zma (A): 20.49100 71.88800 x,y,z range (A): 43.29800 38.35900 51.39700 scale (grids/A): 2.077942 object centre (A): 41.46400 15.58350 46.18950 number of atom coordinates read : 2246 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 90.40926 87.90820 87.82288 assigned negative charge : -303.7472 centred at (gu) : 90.95387 87.97050 87.79781 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 72103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17107 grid for indexing accessible points = 1.400000 m= 29059 mr = 51322 m= 5555 mr = 22159 m= 491 mr = 3740 m= 10 mr = 253 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 29744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 15301 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) : 0.6926475 object centre at (A) : 41.46400 15.58350 46.18950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3160805E-02 3.8220491E-02 midg,1,midg; midg,igrid,midg 2.7015138E-02 1.1583766E-02 1,midg,midg; igrid,midg,midg 4.0481757E-02 1.1778299E-02 gauss-seidel spectral radius is 0.9987857 estimated iterations to convergence 227 setup time was (sec) 0.8500000 now iterating at: 05:28:24 rms-change max change #iterations 4.368171 208.0555 at 10iterations 2.146438 65.14480 at 20iterations 1.047026 35.20972 at 30iterations 0.5159777 16.80238 at 40iterations 0.2526258 7.688224 at 50iterations 0.1237227 3.974910 at 60iterations 6.0682349E-02 1.814901 at 70iterations 2.9812364E-02 0.9161444 at 80iterations 1.4654322E-02 0.4377909 at 90iterations 7.2128889E-03 0.2300873 at 100iterations 3.5722100E-03 0.1093435 at 110iterations 1.7951285E-03 5.6113005E-02 at 120iterations finished qdiffx linear iterations at : 05:28:30 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 1.7951285E-03 5.6113005E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.480000 DelPhi exited at 05:28:31 7.478u 0.159s 0:08.03 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 Tue Oct 11 2011 at 05:28:31 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 = 2246 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: 3.116914 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): 19.81500 63.11300 ymin,ymax (A): -3.596000 34.76300 zmin,zma (A): 20.49100 71.88800 x,y,z range (A): 43.29800 38.35900 51.39700 scale (grids/A): 3.116914 object centre (A): 41.46400 15.58350 46.18950 number of atom coordinates read : 2246 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 90.61382 86.86237 86.73421 assigned negative charge : -303.7472 centred at (gu) : 91.43082 86.95580 86.69675 start vw surface at 0.1600000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 166110 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17107 grid for indexing accessible points = 1.400000 m= 90926 mr = 123516 m= 36714 mr = 75713 m= 10512 mr = 30309 m= 2002 mr = 8223 m= 232 mr = 1520 m= 5 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.760000 number of dielectric boundary points 67062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 15432 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) : 2.077942 object centre at (A) : 41.46400 15.58350 46.18950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4328881 0.2899285 midg,1,midg; midg,igrid,midg 0.2260454 9.6319184E-02 1,midg,midg; igrid,midg,midg 0.3241452 0.2699841 gauss-seidel spectral radius is 0.9992827 estimated iterations to convergence 295 setup time was (sec) 2.050000 now iterating at: 05:28:33 rms-change max change #iterations 9.881930 427.6161 at 10iterations 5.834087 150.7411 at 20iterations 3.430428 74.64209 at 30iterations 2.013709 39.27040 at 40iterations 1.178719 23.14885 at 50iterations 0.6889895 12.78369 at 60iterations 0.4018125 7.253093 at 70iterations 0.2353298 4.704724 at 80iterations 0.1369460 2.579437 at 90iterations 7.9794787E-02 1.438964 at 100iterations 4.6610013E-02 0.8787079 at 110iterations 2.7221594E-02 0.5987082 at 120iterations 1.5946712E-02 0.2835264 at 130iterations 9.4386274E-03 0.1773434 at 140iterations 5.6557562E-03 0.1055107 at 150iterations 3.4644359E-03 6.3053131E-02 at 160iterations 2.2141894E-03 4.2449951E-02 at 170iterations 1.4902041E-03 2.4940491E-02 at 180iterations finished qdiffx linear iterations at : 05:28:43 total time elapsed so far: 12.18000 # loops : 180 mean,max change (kT/e) : 1.4902041E-03 2.4940491E-02 energy calculations done at 12.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.37000 DelPhi exited at 05:28:44 12.368u 0.178s 0:13.14 95.3% 0+0k 0+0io 0pf+0w