Mon Oct 10 14:01:28 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 Mon Oct 10 2011 at 14:01:28 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5855 !!! WARNING: HIR 539 has a net charge of 0.5140 !!! WARNING: HIZ 653 has a net charge of 0.2000 !!! WARNING: ZN7 717 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5001968 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): 25.59800 89.16400 ymin,ymax (A): -84.44400 -13.27200 zmin,zma (A): -30.87200 37.44700 x,y,z range (A): 63.56600 71.17200 68.31900 scale (grids/A): 0.5001968 object centre (A): 57.38100 -48.85800 3.287499 number of atom coordinates read : 5855 total number of charged atoms : 5682 net assigned charge : -3.385955 assigned positive charge : 900.2065 centred at (gu) : 90.88843 90.11015 89.88451 assigned negative charge : -903.6010 centred at (gu) : 90.80382 90.11521 89.79052 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8919 nv = 96 ne = 84 npr = 120847 no. pairs analyzed = 120847 no. exposed pairs = 6792 no. arc points = 47275 no. surface atoms = 2288 nbur = 3567 mkacc time = 0.2600000 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 = 1.680000 m= 322 mr = 4802 m= 0 mr = 5 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.5200000 number of dielectric boundary points 4434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4473 ## 691 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 12129 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3711880E-10 1.5711124E-10 midg,1,midg; midg,igrid,midg -2.0186087E-11 -4.3086045E-11 1,midg,midg; igrid,midg,midg -1.6504495E-10 1.8292924E-10 gauss-seidel spectral radius is 0.9796283 estimated iterations to convergence 58 setup time was (sec) 0.7300000 now iterating at: 14:01:29 rms-change max change #iterations 6.9522068E-02 10.48049 at 10iterations 4.9576689E-03 0.7600222 at 20iterations 9.5270353E-04 0.1818504 at 30iterations 2.7206980E-04 4.9682617E-02 at 40iterations 8.0335310E-05 1.4072418E-02 at 50iterations finished qdiffx linear iterations at : 14:01:32 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 8.0335310E-05 1.4072418E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 14:01:33 3.417u 0.161s 0:04.31 82.8% 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 14:01:33 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5855 !!! WARNING: HIR 539 has a net charge of 0.5140 !!! WARNING: HIZ 653 has a net charge of 0.2000 !!! WARNING: ZN7 717 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.500590 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): 25.59800 89.16400 ymin,ymax (A): -84.44400 -13.27200 zmin,zma (A): -30.87200 37.44700 x,y,z range (A): 63.56600 71.17200 68.31900 scale (grids/A): 1.500590 object centre (A): 57.38100 -48.85800 3.287499 number of atom coordinates read : 5855 total number of charged atoms : 5682 net assigned charge : -3.385955 assigned positive charge : 900.2065 centred at (gu) : 92.66383 90.32874 89.65174 assigned negative charge : -903.6010 centred at (gu) : 92.41152 90.34533 89.37128 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 102206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47275 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 29628 mr = 71652 m= 2503 mr = 20303 m= 42 mr = 1061 m= 0 mr = 1 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 2462 time to turn everything in is 0.7100000 number of dielectric boundary points 41362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 582 ## 15 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 42371 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) : 0.5001968 object centre at (A) : 57.38100 -48.85800 3.287499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4481884E-03 3.4216308E-04 midg,1,midg; midg,igrid,midg -1.7160166E-02 -7.2445571E-03 1,midg,midg; igrid,midg,midg -7.7189235E-03 1.4701391E-02 gauss-seidel spectral radius is 0.9981040 estimated iterations to convergence 183 setup time was (sec) 1.020000 now iterating at: 14:01:34 rms-change max change #iterations 4.157073 166.1367 at 10iterations 1.700511 48.99549 at 20iterations 0.6973870 23.97439 at 30iterations 0.2860463 9.267385 at 40iterations 0.1174546 3.582170 at 50iterations 4.8291605E-02 1.417206 at 60iterations 1.9958761E-02 0.5871520 at 70iterations 8.2749398E-03 0.2341309 at 80iterations 3.4745755E-03 0.1196861 at 90iterations 1.5067792E-03 4.8564911E-02 at 100iterations 6.7880424E-04 2.3298264E-02 at 110iterations 3.2950673E-04 1.2651443E-02 at 120iterations finished qdiffx linear iterations at : 14:01:41 total time elapsed so far: 8.020000 # loops : 120 mean,max change (kT/e) : 3.2950673E-04 1.2651443E-02 energy calculations done at 8.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 14:01:42 8.201u 0.241s 0:09.14 92.3% 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 Mon Oct 10 2011 at 14:01:42 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5855 !!! WARNING: HIR 539 has a net charge of 0.5140 !!! WARNING: HIZ 653 has a net charge of 0.2000 !!! WARNING: ZN7 717 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.250885 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): 25.59800 89.16400 ymin,ymax (A): -84.44400 -13.27200 zmin,zma (A): -30.87200 37.44700 x,y,z range (A): 63.56600 71.17200 68.31900 scale (grids/A): 2.250885 object centre (A): 57.38100 -48.85800 3.287499 number of atom coordinates read : 5855 total number of charged atoms : 5682 net assigned charge : -3.385955 assigned positive charge : 900.2065 centred at (gu) : 93.99529 90.49244 89.47722 assigned negative charge : -903.6010 centred at (gu) : 93.61711 90.51762 89.05692 start vw surface at 0.2100000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 238566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47275 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 106184 mr = 176020 m= 27015 mr = 84009 m= 3598 mr = 19906 m= 156 mr = 2187 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 8258 time to turn everything in is 1.690000 number of dielectric boundary points 93356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 45311 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) : 1.500590 object centre at (A) : 57.38100 -48.85800 3.287499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2499498 -8.9910001E-02 midg,1,midg; midg,igrid,midg -0.4124281 -0.1783978 1,midg,midg; igrid,midg,midg -0.1128113 0.3552370 gauss-seidel spectral radius is 0.9991725 estimated iterations to convergence 275 setup time was (sec) 2.040000 now iterating at: 14:01:44 rms-change max change #iterations 11.22329 299.8038 at 10iterations 6.394269 144.3013 at 20iterations 3.639345 76.25191 at 30iterations 2.053756 40.58312 at 40iterations 1.155239 25.48209 at 50iterations 0.6478473 11.44434 at 60iterations 0.3634434 7.160881 at 70iterations 0.2031063 3.775528 at 80iterations 0.1136631 2.050332 at 90iterations 6.3469954E-02 1.085990 at 100iterations 3.5432294E-02 0.6468678 at 110iterations 1.9785367E-02 0.3988533 at 120iterations 1.1049325E-02 0.2145815 at 130iterations 6.1628250E-03 0.1100521 at 140iterations 3.4379740E-03 5.6861877E-02 at 150iterations 1.9207204E-03 3.3035278E-02 at 160iterations 1.0756585E-03 1.8165588E-02 at 170iterations 6.0342863E-04 1.3891220E-02 at 180iterations finished qdiffx linear iterations at : 14:01:56 total time elapsed so far: 13.61000 # loops : 180 mean,max change (kT/e) : 6.0342863E-04 1.3891220E-02 energy calculations done at 13.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.79000 DelPhi exited at 14:01:57 13.792u 0.245s 0:14.66 95.7% 0+0k 0+0io 0pf+0w