Mon Feb 6 01:23:24 PST 2012 #!/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 Mon Feb 6 2012 at 01:23:25 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 ! Automatically converted by prot2crg.py # of charge parameter records: 961 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1455 !!! WARNING: CYM 48 has a net charge of -0.8000 !!! WARNING: CYM 51 has a net charge of -0.8000 !!! WARNING: CYM 75 has a net charge of -0.8000 !!! WARNING: CYM 139 has a net charge of -0.8000 !!! WARNING: CYM 142 has a net charge of -0.8000 !!! WARNING: HIZ 159 has a net charge of 0.2000 !!! WARNING: ZN 185 has a net charge of 1.4000 !!! WARNING: ZN 186 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6986145 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): -24.40700 26.55100 ymin,ymax (A): -10.04600 31.52600 zmin,zma (A): -34.26300 7.560000 x,y,z range (A): 50.95800 41.57200 41.82300 scale (grids/A): 0.6986145 object centre (A): 1.072000 10.74000 -13.35150 number of atom coordinates read : 1455 total number of charged atoms : 1330 net assigned charge : -2.999996 assigned positive charge : 209.3363 centred at (gu) : 89.20085 90.44061 91.07674 assigned negative charge : -212.3362 centred at (gu) : 89.16740 90.44264 91.02173 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5050 nv = 96 ne = 84 npr = 27559 no. pairs analyzed = 27559 no. exposed pairs = 2189 no. arc points = 16153 no. surface atoms = 721 nbur = 734 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 311 mr = 2308 m= 3 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.1600000 number of dielectric boundary points 3029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1349 ## 100 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5380 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9031240E-08 -6.5070447E-09 midg,1,midg; midg,igrid,midg -1.8387192E-08 -2.2960986E-08 1,midg,midg; igrid,midg,midg -3.4801822E-08 -9.8488169E-09 gauss-seidel spectral radius is 0.9892791 estimated iterations to convergence 79 setup time was (sec) 0.3600000 now iterating at: 01:23:26 rms-change max change #iterations 0.1556231 25.87826 at 10iterations 1.7899513E-02 2.828629 at 20iterations 2.1006921E-03 0.3553848 at 30iterations 2.4672793E-04 4.2243958E-02 at 40iterations 2.9399147E-05 5.0659180E-03 at 50iterations finished qdiffx linear iterations at : 01:23:29 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.9399147E-05 5.0659180E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 01:23:29 3.438u 0.180s 0:05.88 61.3% 0+0k 0+45448io 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 Feb 6 2012 at 01:23:30 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 ! Automatically converted by prot2crg.py # of charge parameter records: 961 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1455 !!! WARNING: CYM 48 has a net charge of -0.8000 !!! WARNING: CYM 51 has a net charge of -0.8000 !!! WARNING: CYM 75 has a net charge of -0.8000 !!! WARNING: CYM 139 has a net charge of -0.8000 !!! WARNING: CYM 142 has a net charge of -0.8000 !!! WARNING: HIZ 159 has a net charge of 0.2000 !!! WARNING: ZN 185 has a net charge of 1.4000 !!! WARNING: ZN 186 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.095844 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): -24.40700 26.55100 ymin,ymax (A): -10.04600 31.52600 zmin,zma (A): -34.26300 7.560000 x,y,z range (A): 50.95800 41.57200 41.82300 scale (grids/A): 2.095844 object centre (A): 1.072000 10.74000 -13.35150 number of atom coordinates read : 1455 total number of charged atoms : 1330 net assigned charge : -2.999996 assigned positive charge : 209.3363 centred at (gu) : 87.60265 91.32216 93.23043 assigned negative charge : -212.3362 centred at (gu) : 87.50235 91.32827 93.06543 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 53164 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16153 grid for indexing accessible points = 1.400000 m= 17946 mr = 33065 m= 2965 mr = 11775 m= 272 mr = 1592 m= 9 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1729 time to turn everything in is 0.3500000 number of dielectric boundary points 27852 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 10562 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) : 0.6986145 object centre at (A) : 1.072000 10.74000 -13.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0644169E-02 -1.4598786E-02 midg,1,midg; midg,igrid,midg -2.9479361E-03 -2.1575300E-02 1,midg,midg; igrid,midg,midg 2.9169838E-03 -1.8996358E-02 gauss-seidel spectral radius is 0.9987604 estimated iterations to convergence 225 setup time was (sec) 0.5700000 now iterating at: 01:23:31 rms-change max change #iterations 3.699717 200.2930 at 10iterations 1.776064 77.13934 at 20iterations 0.8618923 33.66415 at 30iterations 0.4153341 15.98589 at 40iterations 0.2007668 8.040387 at 50iterations 9.6945010E-02 3.513847 at 60iterations 4.6783727E-02 2.103487 at 70iterations 2.2595156E-02 0.8489685 at 80iterations 1.0910342E-02 0.4293890 at 90iterations 5.2641626E-03 0.1939707 at 100iterations 2.5494487E-03 0.1029739 at 110iterations 1.2329640E-03 4.8280716E-02 at 120iterations finished qdiffx linear iterations at : 01:23:38 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 1.2329640E-03 4.8280716E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 01:23:39 7.858u 0.183s 0:08.36 96.0% 0+0k 0+45064io 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 Feb 6 2012 at 01:23:39 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 ! Automatically converted by prot2crg.py # of charge parameter records: 961 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1455 !!! WARNING: CYM 48 has a net charge of -0.8000 !!! WARNING: CYM 51 has a net charge of -0.8000 !!! WARNING: CYM 75 has a net charge of -0.8000 !!! WARNING: CYM 139 has a net charge of -0.8000 !!! WARNING: CYM 142 has a net charge of -0.8000 !!! WARNING: HIZ 159 has a net charge of 0.2000 !!! WARNING: ZN 185 has a net charge of 1.4000 !!! WARNING: ZN 186 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.143765 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): -24.40700 26.55100 ymin,ymax (A): -10.04600 31.52600 zmin,zma (A): -34.26300 7.560000 x,y,z range (A): 50.95800 41.57200 41.82300 scale (grids/A): 3.143765 object centre (A): 1.072000 10.74000 -13.35150 number of atom coordinates read : 1455 total number of charged atoms : 1330 net assigned charge : -2.999996 assigned positive charge : 209.3363 centred at (gu) : 86.40396 91.98329 94.84586 assigned negative charge : -212.3362 centred at (gu) : 86.25358 91.99239 94.59810 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 122682 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16153 grid for indexing accessible points = 1.400000 m= 57258 mr = 80927 m= 20387 mr = 43853 m= 5312 mr = 14946 m= 992 mr = 3571 m= 96 mr = 550 m= 8 mr = 45 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 5781 time to turn everything in is 1.010000 number of dielectric boundary points 62844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 10640 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) : 2.095844 object centre at (A) : 1.072000 10.74000 -13.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2933974E-02 -0.1144290 midg,1,midg; midg,igrid,midg 2.2433152E-02 -0.2170831 1,midg,midg; igrid,midg,midg 0.1216455 -0.2803069 gauss-seidel spectral radius is 0.9992955 estimated iterations to convergence 297 setup time was (sec) 1.230000 now iterating at: 01:23:41 rms-change max change #iterations 8.446866 417.8411 at 10iterations 5.020756 156.1535 at 20iterations 2.976164 72.64287 at 30iterations 1.756591 41.18591 at 40iterations 1.027398 23.56511 at 50iterations 0.6029949 13.52570 at 60iterations 0.3534888 7.617317 at 70iterations 0.2063388 4.489948 at 80iterations 0.1202648 2.512007 at 90iterations 7.0251442E-02 1.720459 at 100iterations 4.0779710E-02 0.9712949 at 110iterations 2.3807101E-02 0.5018387 at 120iterations 1.3811460E-02 0.3326190 at 130iterations 8.0337264E-03 0.1922762 at 140iterations 4.6741799E-03 0.1067162 at 150iterations 2.7163387E-03 5.6235313E-02 at 160iterations 1.5772269E-03 3.2731533E-02 at 170iterations 9.1717957E-04 1.9512177E-02 at 180iterations finished qdiffx linear iterations at : 01:23:52 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 9.1717957E-04 1.9512177E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.56000 DelPhi exited at 01:23:53 12.561u 0.224s 0:13.67 93.4% 0+0k 0+45056io 0pf+0w