Tue Oct 11 04:22:04 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 04:22:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2722 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: 0.6476024 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): -10.81700 37.49500 ymin,ymax (A): -26.20000 22.35000 zmin,zma (A): -8.756000 46.21600 x,y,z range (A): 48.31200 48.55000 54.97200 scale (grids/A): 0.6476024 object centre (A): 13.33900 -1.924999 18.73000 number of atom coordinates read : 2722 total number of charged atoms : 2574 net assigned charge : 2.500024 assigned positive charge : 411.1166 centred at (gu) : 89.87638 90.37283 91.32976 assigned negative charge : -408.6173 centred at (gu) : 89.65356 90.25446 91.34319 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7752 nv = 96 ne = 84 npr = 55340 no. pairs analyzed = 55340 no. exposed pairs = 3381 no. arc points = 23542 no. surface atoms = 1138 nbur = 1584 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4397 m= 4 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.3200000 number of dielectric boundary points 3742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2331 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9182 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0021804E-09 3.2984597E-09 midg,1,midg; midg,igrid,midg -1.2414926E-08 2.3986123E-08 1,midg,midg; igrid,midg,midg -3.0598006E-08 3.6321332E-08 gauss-seidel spectral radius is 0.9876552 estimated iterations to convergence 74 setup time was (sec) 0.6200000 now iterating at: 04:22:05 rms-change max change #iterations 0.1566299 25.63546 at 10iterations 1.6111825E-02 2.525243 at 20iterations 1.6643261E-03 0.2366452 at 30iterations 1.7584482E-04 2.5291443E-02 at 40iterations 2.2450966E-05 3.4561157E-03 at 50iterations finished qdiffx linear iterations at : 04:22:08 total time elapsed so far: 4.360000 # loops : 50 mean,max change (kT/e) : 2.2450966E-05 3.4561157E-03 energy calculations done at 4.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 04:22:09 4.548u 0.374s 0:05.23 93.8% 0+0k 0+0io 6pf+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 04:22:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2722 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: 1.942807 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): -10.81700 37.49500 ymin,ymax (A): -26.20000 22.35000 zmin,zma (A): -8.756000 46.21600 x,y,z range (A): 48.31200 48.55000 54.97200 scale (grids/A): 1.942807 object centre (A): 13.33900 -1.924999 18.73000 number of atom coordinates read : 2722 total number of charged atoms : 2574 net assigned charge : 2.500024 assigned positive charge : 411.1166 centred at (gu) : 89.62830 91.11813 93.98875 assigned negative charge : -408.6173 centred at (gu) : 88.96047 90.76340 94.02924 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23542 grid for indexing accessible points = 1.400000 m= 30827 mr = 58745 m= 4779 mr = 22844 m= 274 mr = 2966 m= 6 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 327 time to turn everything in is 0.6800000 number of dielectric boundary points 34611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 20286 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) : 0.6476024 object centre at (A) : 13.33900 -1.924999 18.73000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2958252E-02 -1.4418584E-02 midg,1,midg; midg,igrid,midg -1.1672833E-02 2.4769943E-02 1,midg,midg; igrid,midg,midg -1.0745423E-02 5.8293175E-02 gauss-seidel spectral radius is 0.9987026 estimated iterations to convergence 220 setup time was (sec) 0.9800000 now iterating at: 04:22:10 rms-change max change #iterations 4.582141 188.8998 at 10iterations 2.201790 88.51908 at 20iterations 1.048423 35.73573 at 30iterations 0.5005816 14.57949 at 40iterations 0.2395911 7.587167 at 50iterations 0.1147211 3.692542 at 60iterations 5.4700326E-02 1.796638 at 70iterations 2.6263336E-02 0.8596406 at 80iterations 1.2519252E-02 0.3671341 at 90iterations 5.9821019E-03 0.1730251 at 100iterations 2.8622262E-03 8.3860397E-02 at 110iterations 1.3750788E-03 4.9526215E-02 at 120iterations finished qdiffx linear iterations at : 04:22:20 total time elapsed so far: 10.89000 # loops : 120 mean,max change (kT/e) : 1.3750788E-03 4.9526215E-02 energy calculations done at 10.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.05000 DelPhi exited at 04:22:21 11.050u 0.465s 0:11.81 97.4% 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 Tue Oct 11 2011 at 04:22:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2722 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: 2.914211 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): -10.81700 37.49500 ymin,ymax (A): -26.20000 22.35000 zmin,zma (A): -8.756000 46.21600 x,y,z range (A): 48.31200 48.55000 54.97200 scale (grids/A): 2.914211 object centre (A): 13.33900 -1.924999 18.73000 number of atom coordinates read : 2722 total number of charged atoms : 2574 net assigned charge : 2.500024 assigned positive charge : 411.1166 centred at (gu) : 89.44241 91.67696 95.98277 assigned negative charge : -408.6173 centred at (gu) : 88.44086 91.14500 96.04361 start vw surface at 0.1300000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 192712 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23542 grid for indexing accessible points = 1.400000 m= 99689 mr = 141862 m= 35936 mr = 81951 m= 8445 mr = 28938 m= 1218 mr = 6291 m= 71 mr = 823 m= 0 mr = 16 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 1087 time to turn everything in is 1.790000 number of dielectric boundary points 78190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 20592 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) : 1.942807 object centre at (A) : 13.33900 -1.924999 18.73000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3147882 5.0355971E-02 midg,1,midg; midg,igrid,midg -0.1316665 0.3092860 1,midg,midg; igrid,midg,midg -6.7354433E-02 0.5221374 gauss-seidel spectral radius is 0.9992735 estimated iterations to convergence 293 setup time was (sec) 2.110000 now iterating at: 04:22:23 rms-change max change #iterations 10.54267 469.8729 at 10iterations 6.182151 142.7902 at 20iterations 3.622182 69.99681 at 30iterations 2.110755 36.91370 at 40iterations 1.228048 27.66535 at 50iterations 0.7142614 14.67991 at 60iterations 0.4151591 8.532871 at 70iterations 0.2409870 4.795424 at 80iterations 0.1400002 2.522827 at 90iterations 8.1116654E-02 1.346645 at 100iterations 4.6982739E-02 0.8131065 at 110iterations 2.7194468E-02 0.4753723 at 120iterations 1.5775142E-02 0.2949104 at 130iterations 9.1544045E-03 0.1755562 at 140iterations 5.3100847E-03 9.0547562E-02 at 150iterations 3.1016413E-03 5.4759979E-02 at 160iterations 1.8161824E-03 3.6538124E-02 at 170iterations 1.0769858E-03 1.9609451E-02 at 180iterations finished qdiffx linear iterations at : 04:22:42 total time elapsed so far: 20.18000 # loops : 180 mean,max change (kT/e) : 1.0769858E-03 1.9609451E-02 energy calculations done at 20.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.37000 DelPhi exited at 04:22:42 20.376u 0.475s 0:21.43 97.2% 0+0k 0+0io 0pf+0w