Wed Dec 28 11:01:36 PST 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 Wed Dec 28 2011 at 11:01:36 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 127 has a net charge of -0.3190 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: 0.5781285 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): -34.96900 10.34900 ymin,ymax (A): 0.2410001 41.80500 zmin,zma (A): -2.949000 58.62900 x,y,z range (A): 45.31800 41.56400 61.57800 scale (grids/A): 0.5781285 object centre (A): -12.31000 21.02300 27.84000 number of atom coordinates read : 2010 total number of charged atoms : 1876 net assigned charge : 3.362005 assigned positive charge : 300.9459 centred at (gu) : 90.37516 89.51871 90.00226 assigned negative charge : -297.5842 centred at (gu) : 90.29101 89.66277 90.00067 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4400 nv = 96 ne = 84 npr = 41123 no. pairs analyzed = 41123 no. exposed pairs = 2586 no. arc points = 18303 no. surface atoms = 871 nbur = 1139 mkacc time = 7.0000008E-02 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 = 1.512000 m= 191 mr = 2312 m= 0 mr = 13 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2266 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1791 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 5560 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5247635E-10 6.9711603E-10 midg,1,midg; midg,igrid,midg 2.9554377E-09 -1.2057508E-09 1,midg,midg; igrid,midg,midg -4.5735518E-10 1.9981532E-09 gauss-seidel spectral radius is 0.9844773 estimated iterations to convergence 66 setup time was (sec) 0.5100000 now iterating at: 11:01:37 rms-change max change #iterations 7.9963490E-02 17.15816 at 10iterations 5.9721023E-03 1.115330 at 20iterations 4.6726948E-04 8.3311081E-02 at 30iterations 3.5249010E-05 7.6980591E-03 at 40iterations 2.7907518E-06 5.8174133E-04 at 50iterations finished qdiffx linear iterations at : 11:01:41 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 2.7907518E-06 5.8174133E-04 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 11:01:42 4.400u 0.420s 0:05.41 89.0% 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 Wed Dec 28 2011 at 11:01:42 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 127 has a net charge of -0.3190 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: 1.734386 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): -34.96900 10.34900 ymin,ymax (A): 0.2410001 41.80500 zmin,zma (A): -2.949000 58.62900 x,y,z range (A): 45.31800 41.56400 61.57800 scale (grids/A): 1.734386 object centre (A): -12.31000 21.02300 27.84000 number of atom coordinates read : 2010 total number of charged atoms : 1876 net assigned charge : 3.362005 assigned positive charge : 300.9459 centred at (gu) : 91.12549 88.55618 90.00677 assigned negative charge : -297.5842 centred at (gu) : 90.87314 88.98878 90.00212 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 47994 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18303 grid for indexing accessible points = 1.400000 m= 15947 mr = 32309 m= 1882 mr = 11499 m= 60 mr = 1053 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 743 time to turn everything in is 0.3000000 number of dielectric boundary points 21020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 202 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 14505 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) : 0.5781285 object centre at (A) : -12.31000 21.02300 27.84000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5368346E-02 2.5726233E-02 midg,1,midg; midg,igrid,midg 4.9403138E-03 -7.0496243E-03 1,midg,midg; igrid,midg,midg -2.2433798E-03 7.7808887E-04 gauss-seidel spectral radius is 0.9982826 estimated iterations to convergence 192 setup time was (sec) 0.6800000 now iterating at: 11:01:43 rms-change max change #iterations 3.041424 166.3343 at 10iterations 1.292385 56.98003 at 20iterations 0.5509055 21.85729 at 30iterations 0.2350120 10.38779 at 40iterations 0.1008402 4.956544 at 50iterations 4.2894762E-02 1.708883 at 60iterations 1.8273309E-02 0.7502880 at 70iterations 7.8088311E-03 0.3412666 at 80iterations 3.3423961E-03 0.1356735 at 90iterations 1.4297967E-03 5.3775787E-02 at 100iterations 6.0947926E-04 2.5096893E-02 at 110iterations 2.5894670E-04 1.0345459E-02 at 120iterations finished qdiffx linear iterations at : 11:01:53 total time elapsed so far: 10.55000 # loops : 120 mean,max change (kT/e) : 2.5894670E-04 1.0345459E-02 energy calculations done at 10.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.67000 DelPhi exited at 11:01:53 10.677u 0.505s 0:11.65 95.8% 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 Wed Dec 28 2011 at 11:01:53 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 127 has a net charge of -0.3190 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: 2.601578 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): -34.96900 10.34900 ymin,ymax (A): 0.2410001 41.80500 zmin,zma (A): -2.949000 58.62900 x,y,z range (A): 45.31800 41.56400 61.57800 scale (grids/A): 2.601578 object centre (A): -12.31000 21.02300 27.84000 number of atom coordinates read : 2010 total number of charged atoms : 1876 net assigned charge : 3.362005 assigned positive charge : 300.9459 centred at (gu) : 91.68818 87.83426 90.01009 assigned negative charge : -297.5842 centred at (gu) : 91.30968 88.48316 90.00334 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 111183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18303 grid for indexing accessible points = 1.400000 m= 53216 mr = 78661 m= 17037 mr = 42965 m= 3161 mr = 13618 m= 296 mr = 2168 m= 13 mr = 167 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 2510 time to turn everything in is 0.6700000 number of dielectric boundary points 47326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 14998 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) : 1.734386 object centre at (A) : -12.31000 21.02300 27.84000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3471201 0.3406832 midg,1,midg; midg,igrid,midg 3.0271692E-02 -9.5530860E-02 1,midg,midg; igrid,midg,midg -4.6527807E-02 -1.8175371E-02 gauss-seidel spectral radius is 0.9991369 estimated iterations to convergence 269 setup time was (sec) 1.030000 now iterating at: 11:01:55 rms-change max change #iterations 7.437459 309.6392 at 10iterations 4.098908 119.7985 at 20iterations 2.259534 54.64611 at 30iterations 1.241174 29.63799 at 40iterations 0.6795678 15.59969 at 50iterations 0.3716722 8.251005 at 60iterations 0.2034582 4.671412 at 70iterations 0.1114852 2.446931 at 80iterations 6.0972899E-02 1.463168 at 90iterations 3.3383925E-02 0.8084450 at 100iterations 1.8323515E-02 0.4606483 at 110iterations 1.0061828E-02 0.2323303 at 120iterations 5.5081979E-03 0.1258659 at 130iterations 2.9994540E-03 6.7398071E-02 at 140iterations 1.6466199E-03 4.0824890E-02 at 150iterations 9.0301380E-04 2.0053148E-02 at 160iterations 4.9485738E-04 1.1078119E-02 at 170iterations 2.7181284E-04 6.0625076E-03 at 180iterations finished qdiffx linear iterations at : 11:02:11 total time elapsed so far: 17.09000 # loops : 180 mean,max change (kT/e) : 2.7181284E-04 6.0625076E-03 energy calculations done at 17.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.22000 DelPhi exited at 11:02:11 17.222u 0.472s 0:18.12 97.6% 0+0k 0+0io 0pf+0w