Mon Oct 10 09:21:36 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+sph.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 = amb.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 Mon Oct 10 2011 at 09:21:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2867 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: 0.5883422 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): -17.82100 33.68100 ymin,ymax (A): -59.78500 -0.2600000 zmin,zma (A): -0.9030000 59.60600 x,y,z range (A): 51.50200 59.52500 60.50900 scale (grids/A): 0.5883422 object centre (A): 7.930000 -30.02250 29.35150 number of atom coordinates read : 2867 total number of charged atoms : 2717 net assigned charge : 9.000020 assigned positive charge : 419.8199 centred at (gu) : 88.20035 88.46117 88.00181 assigned negative charge : -410.8203 centred at (gu) : 88.29881 88.24815 87.87639 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6762 nv = 96 ne = 84 npr = 54656 no. pairs analyzed = 54656 no. exposed pairs = 4449 no. arc points = 31932 no. surface atoms = 1470 nbur = 1397 mkacc time = 9.9999994E-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 = 1.484000 m= 364 mr = 2930 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 4180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3115 ## 313 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8383 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1312509E-09 3.7959471E-09 midg,1,midg; midg,igrid,midg -4.4607433E-09 5.7623142E-09 1,midg,midg; igrid,midg,midg 8.0253439E-09 9.5476342E-11 gauss-seidel spectral radius is 0.9850982 estimated iterations to convergence 67 setup time was (sec) 0.4100000 now iterating at: 09:21:37 rms-change max change #iterations 9.9365681E-02 15.20552 at 10iterations 7.8339754E-03 1.226551 at 20iterations 6.4290134E-04 9.9264145E-02 at 30iterations 5.5320867E-05 7.8821182E-03 at 40iterations 6.5566383E-06 8.7237358E-04 at 50iterations finished qdiffx linear iterations at : 09:21:40 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 6.5566383E-06 8.7237358E-04 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 09:21:40 3.469u 0.159s 0:03.90 92.5% 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 Mon Oct 10 2011 at 09:21:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2867 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: 1.765027 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): -17.82100 33.68100 ymin,ymax (A): -59.78500 -0.2600000 zmin,zma (A): -0.9030000 59.60600 x,y,z range (A): 51.50200 59.52500 60.50900 scale (grids/A): 1.765027 object centre (A): 7.930000 -30.02250 29.35150 number of atom coordinates read : 2867 total number of charged atoms : 2717 net assigned charge : 9.000020 assigned positive charge : 419.8199 centred at (gu) : 84.60085 85.38299 84.00498 assigned negative charge : -410.8203 centred at (gu) : 84.89590 84.74416 83.62878 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31932 grid for indexing accessible points = 1.400000 m= 23071 mr = 43845 m= 2993 mr = 14473 m= 136 mr = 1350 m= 1 mr = 14 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 38780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 21114 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) : 0.5883422 object centre at (A) : 7.930000 -30.02250 29.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3033795E-02 1.1857688E-02 midg,1,midg; midg,igrid,midg 2.0986000E-02 4.1899055E-02 1,midg,midg; igrid,midg,midg 1.3094092E-02 8.0836993E-03 gauss-seidel spectral radius is 0.9984651 estimated iterations to convergence 202 setup time was (sec) 0.5800000 now iterating at: 09:21:41 rms-change max change #iterations 3.750141 172.4242 at 10iterations 1.669791 57.74208 at 20iterations 0.7444785 26.63581 at 30iterations 0.3309510 11.74032 at 40iterations 0.1473025 4.895751 at 50iterations 6.5701626E-02 2.548477 at 60iterations 2.9304367E-02 1.044250 at 70iterations 1.3080316E-02 0.4621277 at 80iterations 5.8371485E-03 0.1935301 at 90iterations 2.6123470E-03 9.3772888E-02 at 100iterations 1.1669829E-03 4.2907715E-02 at 110iterations 5.2160514E-04 1.7962575E-02 at 120iterations finished qdiffx linear iterations at : 09:21:48 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 5.2160514E-04 1.7962575E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 09:21:49 7.933u 0.224s 0:08.58 94.9% 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 Mon Oct 10 2011 at 09:21:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2867 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: 2.647540 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): -17.82100 33.68100 ymin,ymax (A): -59.78500 -0.2600000 zmin,zma (A): -0.9030000 59.60600 x,y,z range (A): 51.50200 59.52500 60.50900 scale (grids/A): 2.647540 object centre (A): 7.930000 -30.02250 29.35150 number of atom coordinates read : 2867 total number of charged atoms : 2717 net assigned charge : 9.000020 assigned positive charge : 419.8199 centred at (gu) : 81.90102 83.07433 81.00752 assigned negative charge : -410.8203 centred at (gu) : 82.34386 82.11623 80.44305 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 166602 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31932 grid for indexing accessible points = 1.400000 m= 75382 mr = 108105 m= 24493 mr = 55856 m= 4928 mr = 17220 m= 484 mr = 2950 m= 23 mr = 191 m= 0 mr = 3 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 87587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 21727 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) : 1.765027 object centre at (A) : 7.930000 -30.02250 29.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1641199E-03 8.6306840E-02 midg,1,midg; midg,igrid,midg 0.4868653 0.4831002 1,midg,midg; igrid,midg,midg 6.6785634E-02 0.1193155 gauss-seidel spectral radius is 0.9992429 estimated iterations to convergence 287 setup time was (sec) 1.160000 now iterating at: 09:21:50 rms-change max change #iterations 9.616302 320.1114 at 10iterations 5.766291 147.7805 at 20iterations 3.386885 78.73470 at 30iterations 1.979291 56.86324 at 40iterations 1.151508 27.07181 at 50iterations 0.6670257 15.75051 at 60iterations 0.3852836 9.124104 at 70iterations 0.2218294 4.851155 at 80iterations 0.1276576 2.656177 at 90iterations 7.3254645E-02 1.477838 at 100iterations 4.1984849E-02 0.8821411 at 110iterations 2.4109751E-02 0.5297306 at 120iterations 1.3766199E-02 0.2786024 at 130iterations 7.8835217E-03 0.1539440 at 140iterations 4.5035873E-03 9.2872620E-02 at 150iterations 2.5751849E-03 5.1479340E-02 at 160iterations 1.4713658E-03 2.7758360E-02 at 170iterations 8.4038702E-04 1.5827179E-02 at 180iterations finished qdiffx linear iterations at : 09:22:02 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 8.4038702E-04 1.5827179E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 09:22:02 12.889u 0.207s 0:13.36 97.9% 0+0k 0+0io 0pf+0w