Sun Oct 9 23:55:32 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 23:55:32 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2490 !!! WARNING: SEP 674 has a net charge of -0.4750 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: 0.6235768 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): -7.693000 49.39700 ymin,ymax (A): -25.55400 22.02900 zmin,zma (A): -8.497000 40.46100 x,y,z range (A): 57.09000 47.58300 48.95800 scale (grids/A): 0.6235768 object centre (A): 20.85200 -1.762500 15.98200 number of atom coordinates read : 2490 total number of charged atoms : 2421 net assigned charge : 2.525008 assigned positive charge : 388.1039 centred at (gu) : 89.62303 90.35188 88.09840 assigned negative charge : -385.5797 centred at (gu) : 89.52811 90.40820 88.09158 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6346 nv = 96 ne = 84 npr = 49095 no. pairs analyzed = 49095 no. exposed pairs = 3146 no. arc points = 22179 no. surface atoms = 1062 nbur = 1428 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3405 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3000000 number of dielectric boundary points 3241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2281 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8041 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7183193E-09 1.8823176E-09 midg,1,midg; midg,igrid,midg 5.9239897E-09 -1.9740369E-09 1,midg,midg; igrid,midg,midg -5.1008682E-09 8.4365377E-09 gauss-seidel spectral radius is 0.9866703 estimated iterations to convergence 71 setup time was (sec) 0.5500000 now iterating at: 23:55:32 rms-change max change #iterations 0.1257474 19.87909 at 10iterations 1.1589024E-02 1.991402 at 20iterations 1.0940910E-03 0.1585121 at 30iterations 1.0254611E-04 1.6234875E-02 at 40iterations 9.4560846E-06 1.6365051E-03 at 50iterations finished qdiffx linear iterations at : 23:55:35 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 9.4560846E-06 1.6365051E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 23:55:36 3.469u 0.189s 0:03.96 91.9% 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 23:55:36 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2490 !!! WARNING: SEP 674 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.870730 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): -7.693000 49.39700 ymin,ymax (A): -25.55400 22.02900 zmin,zma (A): -8.497000 40.46100 x,y,z range (A): 57.09000 47.58300 48.95800 scale (grids/A): 1.870730 object centre (A): 20.85200 -1.762500 15.98200 number of atom coordinates read : 2490 total number of charged atoms : 2421 net assigned charge : 2.525008 assigned positive charge : 388.1039 centred at (gu) : 88.86852 91.05502 84.29463 assigned negative charge : -385.5797 centred at (gu) : 88.58443 91.22455 84.27455 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 69753 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22179 grid for indexing accessible points = 1.400000 m= 23354 mr = 47897 m= 2884 mr = 16767 m= 92 mr = 1618 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1717 time to turn everything in is 0.5400000 number of dielectric boundary points 29789 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19043 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) : 0.6235768 object centre at (A) : 20.85200 -1.762500 15.98200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4209679E-02 3.3242413E-04 midg,1,midg; midg,igrid,midg 2.5245601E-03 4.9977712E-03 1,midg,midg; igrid,midg,midg -2.9742900E-02 3.3227053E-02 gauss-seidel spectral radius is 0.9985684 estimated iterations to convergence 210 setup time was (sec) 0.8700000 now iterating at: 23:55:37 rms-change max change #iterations 4.036035 176.5720 at 10iterations 1.857591 69.41998 at 20iterations 0.8532677 29.96549 at 30iterations 0.3916989 14.38489 at 40iterations 0.1800987 6.496337 at 50iterations 8.2907327E-02 2.909348 at 60iterations 3.7864864E-02 1.323650 at 70iterations 1.7439663E-02 0.5758839 at 80iterations 8.0243750E-03 0.2559690 at 90iterations 3.6909557E-03 0.1384640 at 100iterations 1.6986592E-03 5.5204153E-02 at 110iterations 7.8090047E-04 2.6023865E-02 at 120iterations finished qdiffx linear iterations at : 23:55:44 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 7.8090047E-04 2.6023865E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 23:55:44 7.997u 0.216s 0:08.53 96.1% 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 23:55:44 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2490 !!! WARNING: SEP 674 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.806096 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): -7.693000 49.39700 ymin,ymax (A): -25.55400 22.02900 zmin,zma (A): -8.497000 40.46100 x,y,z range (A): 57.09000 47.58300 48.95800 scale (grids/A): 2.806096 object centre (A): 20.85200 -1.762500 15.98200 number of atom coordinates read : 2490 total number of charged atoms : 2421 net assigned charge : 2.525008 assigned positive charge : 388.1039 centred at (gu) : 88.30253 91.58231 81.44191 assigned negative charge : -385.5797 centred at (gu) : 87.87660 91.83677 81.41181 start vw surface at 0.1900000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 161378 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22179 grid for indexing accessible points = 1.400000 m= 77985 mr = 116022 m= 25178 mr = 63255 m= 4990 mr = 19740 m= 467 mr = 3511 m= 10 mr = 255 m= 0 mr = 2 time to grow re-entrant surface = 0.7600001 no. cavity mid-points inaccessible to solvent = 5534 time to turn everything in is 1.370000 number of dielectric boundary points 67223 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 19367 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) : 1.870730 object centre at (A) : 20.85200 -1.762500 15.98200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1351044 -7.0564952E-03 midg,1,midg; midg,igrid,midg 2.4598012E-02 0.1111700 1,midg,midg; igrid,midg,midg -0.4934230 0.3829030 gauss-seidel spectral radius is 0.9992452 estimated iterations to convergence 287 setup time was (sec) 1.700000 now iterating at: 23:55:46 rms-change max change #iterations 9.506727 357.4166 at 10iterations 5.464883 117.2565 at 20iterations 3.114707 65.46648 at 30iterations 1.779873 35.48689 at 40iterations 1.016479 18.79790 at 50iterations 0.5790178 11.50439 at 60iterations 0.3298948 7.701877 at 70iterations 0.1878226 3.743360 at 80iterations 0.1070396 2.089142 at 90iterations 6.0853139E-02 1.107503 at 100iterations 3.4719493E-02 0.6277161 at 110iterations 1.9814992E-02 0.4032469 at 120iterations 1.1276518E-02 0.2265137 at 130iterations 6.4369943E-03 0.1201706 at 140iterations 3.6665222E-03 7.6582670E-02 at 150iterations 2.0843458E-03 4.0382385E-02 at 160iterations 1.1901729E-03 2.2126198E-02 at 170iterations 6.7952846E-04 1.2385368E-02 at 180iterations finished qdiffx linear iterations at : 23:55:57 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 6.7952846E-04 1.2385368E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 23:55:58 12.840u 0.226s 0:13.35 97.8% 0+0k 0+0io 0pf+0w