Sun Oct 9 18:45:21 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 18:45:21 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3270 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: 0.5073032 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): -8.490000 61.68500 ymin,ymax (A): -13.73500 35.07900 zmin,zma (A): 18.94100 69.64000 x,y,z range (A): 70.17500 48.81400 50.69900 scale (grids/A): 0.5073032 object centre (A): 26.59750 10.67200 44.29050 number of atom coordinates read : 3270 total number of charged atoms : 3124 net assigned charge : 11.00003 assigned positive charge : 503.8377 centred at (gu) : 90.65207 89.84500 89.37132 assigned negative charge : -492.8391 centred at (gu) : 90.71439 89.93038 89.33112 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5273 nv = 96 ne = 84 npr = 65492 no. pairs analyzed = 65492 no. exposed pairs = 4198 no. arc points = 28915 no. surface atoms = 1413 nbur = 1857 mkacc time = 0.1600000 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 = 1.680000 m= 193 mr = 2635 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 2829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2875 ## 470 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7164 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5171876E-11 1.6785066E-10 midg,1,midg; midg,igrid,midg 2.7782221E-10 1.6599509E-12 1,midg,midg; igrid,midg,midg 1.9530069E-10 4.4096476E-11 gauss-seidel spectral radius is 0.9800192 estimated iterations to convergence 58 setup time was (sec) 0.6000000 now iterating at: 18:45:22 rms-change max change #iterations 5.4411463E-02 9.828392 at 10iterations 3.2731111E-03 0.5275669 at 20iterations 5.0874671E-04 8.0680847E-02 at 30iterations 2.3424061E-04 3.9445877E-02 at 40iterations 1.1836516E-04 2.0238876E-02 at 50iterations finished qdiffx linear iterations at : 18:45:25 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.1836516E-04 2.0238876E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 18:45:25 3.405u 0.158s 0:03.86 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 18:45:25 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 # of charge parameter records: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3270 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: 1.521909 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): -8.490000 61.68500 ymin,ymax (A): -13.73500 35.07900 zmin,zma (A): 18.94100 69.64000 x,y,z range (A): 70.17500 48.81400 50.69900 scale (grids/A): 1.521909 object centre (A): 26.59750 10.67200 44.29050 number of atom coordinates read : 3270 total number of charged atoms : 3124 net assigned charge : 11.00003 assigned positive charge : 503.8377 centred at (gu) : 91.95525 89.53389 88.11324 assigned negative charge : -492.8391 centred at (gu) : 92.14279 89.79070 87.99296 start vw surface at 0.1800000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 59674 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28915 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 17229 mr = 40346 m= 1426 mr = 11066 m= 29 mr = 494 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 26452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 430 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 23398 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) : 0.5073032 object centre at (A) : 26.59750 10.67200 44.29050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7425409E-03 4.7424799E-03 midg,1,midg; midg,igrid,midg 5.7054865E-03 -1.7613556E-03 1,midg,midg; igrid,midg,midg 2.4059389E-02 -5.4370258E-03 gauss-seidel spectral radius is 0.9979191 estimated iterations to convergence 174 setup time was (sec) 0.7700000 now iterating at: 18:45:26 rms-change max change #iterations 3.038711 152.1579 at 10iterations 1.188118 53.59041 at 20iterations 0.4676812 19.05100 at 30iterations 0.1842083 7.350922 at 40iterations 7.2323032E-02 2.837601 at 50iterations 2.8532576E-02 1.084574 at 60iterations 1.1321875E-02 0.4676895 at 70iterations 4.5780540E-03 0.1696930 at 80iterations 1.9842319E-03 8.3898067E-02 at 90iterations 1.0220006E-03 4.3478489E-02 at 100iterations 6.5947382E-04 2.4652481E-02 at 110iterations 4.8517229E-04 1.6943216E-02 at 120iterations finished qdiffx linear iterations at : 18:45:32 total time elapsed so far: 7.130000 # loops : 120 mean,max change (kT/e) : 4.8517229E-04 1.6943216E-02 energy calculations done at 7.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.320000 DelPhi exited at 18:45:33 7.323u 0.158s 0:07.81 95.6% 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 18:45:33 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 = 3270 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.282864 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): -8.490000 61.68500 ymin,ymax (A): -13.73500 35.07900 zmin,zma (A): 18.94100 69.64000 x,y,z range (A): 70.17500 48.81400 50.69900 scale (grids/A): 2.282864 object centre (A): 26.59750 10.67200 44.29050 number of atom coordinates read : 3270 total number of charged atoms : 3124 net assigned charge : 11.00003 assigned positive charge : 503.8377 centred at (gu) : 92.93269 89.30070 87.16975 assigned negative charge : -492.8391 centred at (gu) : 93.21414 89.68594 86.98923 start vw surface at 0.1600000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 138809 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28915 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 61355 mr = 99215 m= 15446 mr = 46946 m= 1941 mr = 10675 m= 82 mr = 988 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.070000 number of dielectric boundary points 59786 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 24908 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) : 1.521909 object centre at (A) : 26.59750 10.67200 44.29050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1570477 6.9740750E-02 midg,1,midg; midg,igrid,midg 8.2411110E-02 -5.9100065E-02 1,midg,midg; igrid,midg,midg 0.7511877 -0.2163827 gauss-seidel spectral radius is 0.9990555 estimated iterations to convergence 257 setup time was (sec) 1.390000 now iterating at: 18:45:35 rms-change max change #iterations 8.266547 287.9439 at 10iterations 4.561587 122.3275 at 20iterations 2.505362 63.05207 at 30iterations 1.361436 34.09829 at 40iterations 0.7396380 19.08305 at 50iterations 0.4009492 11.39026 at 60iterations 0.2169129 5.782652 at 70iterations 0.1172489 2.734875 at 80iterations 6.2803753E-02 1.439098 at 90iterations 3.3882961E-02 0.8311520 at 100iterations 1.8244362E-02 0.4544353 at 110iterations 9.8012974E-03 0.2434120 at 120iterations 5.2491603E-03 0.1164513 at 130iterations 2.8165765E-03 6.5624237E-02 at 140iterations 1.5121836E-03 4.0135384E-02 at 150iterations 8.1303302E-04 1.8684506E-02 at 160iterations 4.3720624E-04 9.6302032E-03 at 170iterations 2.3702440E-04 6.6671371E-03 at 180iterations finished qdiffx linear iterations at : 18:45:45 total time elapsed so far: 11.40000 # loops : 180 mean,max change (kT/e) : 2.3702440E-04 6.6671371E-03 energy calculations done at 11.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.59000 DelPhi exited at 18:45:45 11.593u 0.164s 0:12.03 97.6% 0+0k 0+0io 0pf+0w