Sat Oct 15 15:39:08 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 Sat Oct 15 2011 at 15:39:09 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6373532 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): -1.986000 53.87000 ymin,ymax (A): -22.55100 25.78700 zmin,zma (A): 9.112000 55.00700 x,y,z range (A): 55.85600 48.33800 45.89500 scale (grids/A): 0.6373532 object centre (A): 25.94200 1.617999 32.05950 number of atom coordinates read : 2392 total number of charged atoms : 2254 net assigned charge : 6.039007 assigned positive charge : 364.7965 centred at (gu) : 88.72141 89.32056 89.91412 assigned negative charge : -358.7577 centred at (gu) : 88.76900 89.28807 89.74341 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6593 nv = 96 ne = 84 npr = 48067 no. pairs analyzed = 48067 no. exposed pairs = 2902 no. arc points = 20264 no. surface atoms = 989 nbur = 1403 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 353 mr = 3693 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2008 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7797 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.4792627E-09 2.4440585E-08 midg,1,midg; midg,igrid,midg 5.5628395E-09 9.8531059E-09 1,midg,midg; igrid,midg,midg 1.6893267E-08 2.6155955E-09 gauss-seidel spectral radius is 0.9872283 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 15:39:10 rms-change max change #iterations 0.1439657 23.10904 at 10iterations 1.4598023E-02 2.018606 at 20iterations 1.7648814E-03 0.2656326 at 30iterations 2.8593527E-04 4.4845581E-02 at 40iterations 6.0984101E-05 9.7045898E-03 at 50iterations finished qdiffx linear iterations at : 15:39:16 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 6.0984101E-05 9.7045898E-03 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 15:39:16 3.732u 0.215s 0:06.92 56.9% 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 Sat Oct 15 2011 at 15:39:16 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.912059 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): -1.986000 53.87000 ymin,ymax (A): -22.55100 25.78700 zmin,zma (A): 9.112000 55.00700 x,y,z range (A): 55.85600 48.33800 45.89500 scale (grids/A): 1.912059 object centre (A): 25.94200 1.617999 32.05950 number of atom coordinates read : 2392 total number of charged atoms : 2254 net assigned charge : 6.039007 assigned positive charge : 364.7965 centred at (gu) : 86.16392 87.96148 89.74218 assigned negative charge : -358.7577 centred at (gu) : 86.30684 87.86418 89.23001 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20264 grid for indexing accessible points = 1.400000 m= 26604 mr = 49204 m= 4178 mr = 19967 m= 260 mr = 2533 m= 5 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 29724 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 17726 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) : 0.6373532 object centre at (A) : 25.94200 1.617999 32.05950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2347055E-02 3.8864512E-02 midg,1,midg; midg,igrid,midg 1.1534954E-03 5.0294236E-03 1,midg,midg; igrid,midg,midg 2.2749182E-02 2.6059793E-02 gauss-seidel spectral radius is 0.9986260 estimated iterations to convergence 214 setup time was (sec) 0.6000000 now iterating at: 15:39:17 rms-change max change #iterations 4.115434 188.8594 at 10iterations 1.926448 70.14314 at 20iterations 0.9088140 35.13865 at 30iterations 0.4243300 13.38985 at 40iterations 0.1986406 6.298893 at 50iterations 9.3239583E-02 2.884615 at 60iterations 4.3734226E-02 1.389053 at 70iterations 2.0571414E-02 0.7069473 at 80iterations 9.6889203E-03 0.3254865 at 90iterations 4.5643356E-03 0.1630058 at 100iterations 2.1845531E-03 6.9221497E-02 at 110iterations 1.0552746E-03 3.4236908E-02 at 120iterations finished qdiffx linear iterations at : 15:39:34 total time elapsed so far: 8.500000 # loops : 120 mean,max change (kT/e) : 1.0552746E-03 3.4236908E-02 energy calculations done at 8.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.640000 DelPhi exited at 15:39:37 8.640u 0.283s 0:20.37 43.7% 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 Sat Oct 15 2011 at 15:39:37 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.868089 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): -1.986000 53.87000 ymin,ymax (A): -22.55100 25.78700 zmin,zma (A): 9.112000 55.00700 x,y,z range (A): 55.85600 48.33800 45.89500 scale (grids/A): 2.868089 object centre (A): 25.94200 1.617999 32.05950 number of atom coordinates read : 2392 total number of charged atoms : 2254 net assigned charge : 6.039007 assigned positive charge : 364.7965 centred at (gu) : 84.24586 86.94218 89.61320 assigned negative charge : -358.7577 centred at (gu) : 84.46016 86.79623 88.84502 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 162695 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20264 grid for indexing accessible points = 1.400000 m= 84992 mr = 118802 m= 31713 mr = 70462 m= 7391 mr = 25604 m= 1077 mr = 5478 m= 86 mr = 673 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 66889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 18022 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) : 1.912059 object centre at (A) : 25.94200 1.617999 32.05950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3217171 0.4082715 midg,1,midg; midg,igrid,midg -2.1564249E-02 -1.6865153E-02 1,midg,midg; igrid,midg,midg 5.0448209E-02 0.2239274 gauss-seidel spectral radius is 0.9992486 estimated iterations to convergence 288 setup time was (sec) 1.260000 now iterating at: 15:39:39 rms-change max change #iterations 9.670489 377.2183 at 10iterations 5.641435 160.7756 at 20iterations 3.267380 79.36258 at 30iterations 1.890593 46.88522 at 40iterations 1.089531 21.40664 at 50iterations 0.6268058 13.00777 at 60iterations 0.3599291 7.258842 at 70iterations 0.2068866 4.218208 at 80iterations 0.1187975 2.217489 at 90iterations 6.8149820E-02 1.374338 at 100iterations 3.9043639E-02 0.7717390 at 110iterations 2.2424128E-02 0.4295826 at 120iterations 1.2880747E-02 0.2736320 at 130iterations 7.4262214E-03 0.1379108 at 140iterations 4.3015974E-03 8.5872650E-02 at 150iterations 2.5121414E-03 4.7185898E-02 at 160iterations 1.4943333E-03 2.7209759E-02 at 170iterations 9.0956595E-04 1.7349243E-02 at 180iterations finished qdiffx linear iterations at : 15:40:05 total time elapsed so far: 13.82000 # loops : 180 mean,max change (kT/e) : 9.0956595E-04 1.7349243E-02 energy calculations done at 13.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.95000 DelPhi exited at 15:40:05 13.953u 0.313s 0:28.62 49.8% 0+0k 0+0io 0pf+0w