Tue Oct 11 06:13:58 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 Tue Oct 11 2011 at 06:13:58 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2037 !!! WARNING: SEP 190 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7044204 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): 27.12100 70.64700 ymin,ymax (A): 43.92200 81.20200 zmin,zma (A): -60.25700 -9.719001 x,y,z range (A): 43.52600 37.28001 50.53800 scale (grids/A): 0.7044204 object centre (A): 48.88400 62.56200 -34.98800 number of atom coordinates read : 2037 total number of charged atoms : 1910 net assigned charge : 6.025011 assigned positive charge : 309.0171 centred at (gu) : 90.61325 89.71982 89.05274 assigned negative charge : -302.9922 centred at (gu) : 90.79120 89.76301 89.06756 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6976 nv = 96 ne = 84 npr = 40244 no. pairs analyzed = 40244 no. exposed pairs = 2595 no. arc points = 17639 no. surface atoms = 881 nbur = 1156 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 477 mr = 3942 m= 2 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1568 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7605 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5209775E-08 3.4481562E-08 midg,1,midg; midg,igrid,midg 7.0761629E-08 2.6929076E-08 1,midg,midg; igrid,midg,midg 1.1190446E-07 -3.8240046E-08 gauss-seidel spectral radius is 0.9894939 estimated iterations to convergence 79 setup time was (sec) 0.5300000 now iterating at: 06:13:59 rms-change max change #iterations 0.1958329 27.27716 at 10iterations 2.4945855E-02 3.439182 at 20iterations 3.5882122E-03 0.5691299 at 30iterations 8.1012625E-04 9.2475891E-02 at 40iterations 2.5404227E-04 2.8957367E-02 at 50iterations finished qdiffx linear iterations at : 06:14:03 total time elapsed so far: 4.200000 # loops : 50 mean,max change (kT/e) : 2.5404227E-04 2.8957367E-02 energy calculations done at 4.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.360000 DelPhi exited at 06:14:03 4.364u 0.416s 0:05.10 93.5% 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 06:14:04 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2037 !!! WARNING: SEP 190 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.113261 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): 27.12100 70.64700 ymin,ymax (A): 43.92200 81.20200 zmin,zma (A): -60.25700 -9.719001 x,y,z range (A): 43.52600 37.28001 50.53800 scale (grids/A): 2.113261 object centre (A): 48.88400 62.56200 -34.98800 number of atom coordinates read : 2037 total number of charged atoms : 1910 net assigned charge : 6.025011 assigned positive charge : 309.0171 centred at (gu) : 91.83981 89.15961 87.15827 assigned negative charge : -302.9922 centred at (gu) : 92.37386 89.28914 87.20267 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73881 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17639 grid for indexing accessible points = 1.400000 m= 30522 mr = 52290 m= 5898 mr = 22912 m= 520 mr = 3830 m= 11 mr = 235 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 31565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15166 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) : 0.7044204 object centre at (A) : 48.88400 62.56200 -34.98800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9501250E-02 2.1161269E-02 midg,1,midg; midg,igrid,midg 2.7633658E-02 7.1240352E-03 1,midg,midg; igrid,midg,midg 3.7879225E-02 1.0599238E-02 gauss-seidel spectral radius is 0.9988214 estimated iterations to convergence 231 setup time was (sec) 0.9100000 now iterating at: 06:14:05 rms-change max change #iterations 4.508771 198.7296 at 10iterations 2.236309 78.11528 at 20iterations 1.103390 36.40621 at 30iterations 0.5438233 17.02916 at 40iterations 0.2714145 8.890995 at 50iterations 0.1340586 4.260816 at 60iterations 6.6623785E-02 2.039160 at 70iterations 3.3220880E-02 0.9642162 at 80iterations 1.6695404E-02 0.5356903 at 90iterations 8.5009076E-03 0.2462730 at 100iterations 4.4359425E-03 0.1357956 at 110iterations 2.4325426E-03 7.3440552E-02 at 120iterations finished qdiffx linear iterations at : 06:14:14 total time elapsed so far: 10.32000 # loops : 120 mean,max change (kT/e) : 2.4325426E-03 7.3440552E-02 energy calculations done at 10.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.47000 DelPhi exited at 06:14:15 10.478u 0.453s 0:11.26 96.9% 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 Tue Oct 11 2011 at 06:14:15 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2037 !!! WARNING: SEP 190 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.169892 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): 27.12100 70.64700 ymin,ymax (A): 43.92200 81.20200 zmin,zma (A): -60.25700 -9.719001 x,y,z range (A): 43.52600 37.28001 50.53800 scale (grids/A): 3.169892 object centre (A): 48.88400 62.56200 -34.98800 number of atom coordinates read : 2037 total number of charged atoms : 1910 net assigned charge : 6.025011 assigned positive charge : 309.0171 centred at (gu) : 92.75970 88.73949 85.73743 assigned negative charge : -302.9922 centred at (gu) : 93.56091 88.93374 85.80395 start vw surface at 7.740000 fill in re-entrant regions at 8.390000 boundary points on vw surface= 169877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17639 grid for indexing accessible points = 1.400000 m= 94452 mr = 125604 m= 39080 mr = 78353 m= 10980 mr = 31700 m= 2033 mr = 8321 m= 204 mr = 1353 m= 6 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 9.550000 number of dielectric boundary points 71200 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 9.800000 number of grid points assigned charge 15280 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) : 2.113261 object centre at (A) : 48.88400 62.56200 -34.98800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2761618 3.2237206E-02 midg,1,midg; midg,igrid,midg 0.2247433 4.9397361E-02 1,midg,midg; igrid,midg,midg 0.3165277 0.1956954 gauss-seidel spectral radius is 0.9992934 estimated iterations to convergence 297 setup time was (sec) 9.990000 now iterating at: 06:14:25 rms-change max change #iterations 10.14192 381.7990 at 10iterations 6.037906 161.8223 at 20iterations 3.581224 65.76859 at 30iterations 2.116762 40.44541 at 40iterations 1.248380 26.89851 at 50iterations 0.7338453 13.69245 at 60iterations 0.4317316 7.664316 at 70iterations 0.2539443 4.768135 at 80iterations 0.1489650 2.722282 at 90iterations 8.7570481E-02 1.528149 at 100iterations 5.1479261E-02 0.9868431 at 110iterations 3.0566970E-02 0.6790134 at 120iterations 1.8427929E-02 0.3466072 at 130iterations 1.1351781E-02 0.2118855 at 140iterations 7.3035844E-03 0.1270142 at 150iterations 4.9603842E-03 9.0347290E-02 at 160iterations 3.6006451E-03 6.4437866E-02 at 170iterations 2.7718488E-03 4.7378540E-02 at 180iterations finished qdiffx linear iterations at : 06:14:41 total time elapsed so far: 25.83000 # loops : 180 mean,max change (kT/e) : 2.7718488E-03 4.7378540E-02 energy calculations done at 25.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 25.99000 DelPhi exited at 06:14:42 25.996u 0.512s 0:27.02 98.0% 0+0k 0+0io 0pf+0w