Sat Oct 15 15:07:56 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 15:07:56 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1165 !!! WARNING: HIT 60 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7483393 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): -6.410000 32.23100 ymin,ymax (A): 1.263000 39.96200 zmin,zma (A): -1.640000 45.93200 x,y,z range (A): 38.64100 38.69900 47.57200 scale (grids/A): 0.7483393 object centre (A): 12.91050 20.61250 22.14600 number of atom coordinates read : 1165 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 179.7651 centred at (gu) : 88.63546 89.37465 88.39032 assigned negative charge : -174.2512 centred at (gu) : 88.35503 89.34678 88.44048 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4397 nv = 96 ne = 84 npr = 22714 no. pairs analyzed = 22714 no. exposed pairs = 1499 no. arc points = 10799 no. surface atoms = 504 nbur = 661 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 281 mr = 2253 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.1200000 number of dielectric boundary points 2367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 860 ## 79 charges are in solution ## iepsmp to db, and charging done at 0.1700000 number of grid points assigned charge 4519 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0240186E-07 6.4796829E-08 midg,1,midg; midg,igrid,midg 1.1185340E-07 1.2194779E-07 1,midg,midg; igrid,midg,midg -9.2442598E-08 2.3044313E-07 gauss-seidel spectral radius is 0.9905958 estimated iterations to convergence 84 setup time was (sec) 0.3000000 now iterating at: 15:07:56 rms-change max change #iterations 0.1936554 30.88259 at 10iterations 2.5806878E-02 4.429552 at 20iterations 3.5257377E-03 0.6205940 at 30iterations 4.6897650E-04 7.7049255E-02 at 40iterations 6.3978638E-05 1.1096954E-02 at 50iterations finished qdiffx linear iterations at : 15:07:59 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 6.3978638E-05 1.1096954E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 15:08:00 3.304u 0.215s 0:03.93 89.3% 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 15:08:00 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1165 !!! WARNING: HIT 60 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.245018 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): -6.410000 32.23100 ymin,ymax (A): 1.263000 39.96200 zmin,zma (A): -1.640000 45.93200 x,y,z range (A): 38.64100 38.69900 47.57200 scale (grids/A): 2.245018 object centre (A): 12.91050 20.61250 22.14600 number of atom coordinates read : 1165 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 179.7651 centred at (gu) : 85.90644 88.12386 85.17106 assigned negative charge : -174.2512 centred at (gu) : 85.06524 88.04047 85.32159 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 46401 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10799 grid for indexing accessible points = 1.400000 m= 17520 mr = 30297 m= 3393 mr = 13105 m= 297 mr = 2326 m= 16 mr = 159 m= 0 mr = 9 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 1277 time to turn everything in is 0.2500000 number of dielectric boundary points 21731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8462 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) : 0.7483393 object centre at (A) : 12.91050 20.61250 22.14600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6356386E-02 4.7145882E-03 midg,1,midg; midg,igrid,midg 3.7611760E-02 3.1276714E-02 1,midg,midg; igrid,midg,midg -2.7787045E-02 3.9086170E-02 gauss-seidel spectral radius is 0.9988541 estimated iterations to convergence 234 setup time was (sec) 0.4600000 now iterating at: 15:08:00 rms-change max change #iterations 3.764540 170.7688 at 10iterations 1.879589 81.57079 at 20iterations 0.9361956 33.29044 at 30iterations 0.4669841 20.61414 at 40iterations 0.2314955 8.237834 at 50iterations 0.1160293 4.353657 at 60iterations 5.7227280E-02 2.169258 at 70iterations 2.8606813E-02 1.142401 at 80iterations 1.4298353E-02 0.5081720 at 90iterations 7.0972075E-03 0.2535095 at 100iterations 3.5245703E-03 0.1261292 at 110iterations 1.7524342E-03 6.6177368E-02 at 120iterations finished qdiffx linear iterations at : 15:08:08 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 1.7524342E-03 6.6177368E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 15:08:08 7.751u 0.231s 0:08.46 94.3% 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 15:08:08 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1165 !!! WARNING: HIT 60 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.367527 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): -6.410000 32.23100 ymin,ymax (A): 1.263000 39.96200 zmin,zma (A): -1.640000 45.93200 x,y,z range (A): 38.64100 38.69900 47.57200 scale (grids/A): 3.367527 object centre (A): 12.91050 20.61250 22.14600 number of atom coordinates read : 1165 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 179.7651 centred at (gu) : 83.85974 87.18583 82.75658 assigned negative charge : -174.2512 centred at (gu) : 82.59789 87.06079 82.98239 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 106804 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10799 grid for indexing accessible points = 1.400000 m= 53644 mr = 73498 m= 22187 mr = 43639 m= 6472 mr = 18281 m= 1207 mr = 5145 m= 172 mr = 943 m= 18 mr = 128 m= 0 mr = 14 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 4270 time to turn everything in is 0.7300000 number of dielectric boundary points 48856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 8488 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) : 2.245018 object centre at (A) : 12.91050 20.61250 22.14600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3894242 4.9122047E-02 midg,1,midg; midg,igrid,midg 0.3159351 0.2494529 1,midg,midg; igrid,midg,midg -0.2107830 0.2741041 gauss-seidel spectral radius is 0.9992941 estimated iterations to convergence 297 setup time was (sec) 0.9900000 now iterating at: 15:08:09 rms-change max change #iterations 8.179105 248.2810 at 10iterations 4.772086 126.3045 at 20iterations 2.764756 67.76061 at 30iterations 1.602290 36.05488 at 40iterations 0.9318496 21.09076 at 50iterations 0.5396437 11.01515 at 60iterations 0.3117495 6.672251 at 70iterations 0.1811200 3.988827 at 80iterations 0.1052744 2.354141 at 90iterations 6.1062105E-02 1.463732 at 100iterations 3.5333447E-02 0.7783813 at 110iterations 2.0530706E-02 0.4132843 at 120iterations 1.1879344E-02 0.2454071 at 130iterations 6.9095534E-03 0.1417615 at 140iterations 4.0047872E-03 8.6870670E-02 at 150iterations 2.3261458E-03 5.1183701E-02 at 160iterations 1.3512261E-03 2.8617859E-02 at 170iterations 7.8421360E-04 1.7952919E-02 at 180iterations finished qdiffx linear iterations at : 15:08:21 total time elapsed so far: 12.13000 # loops : 180 mean,max change (kT/e) : 7.8421360E-04 1.7952919E-02 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 15:08:21 12.256u 0.254s 0:12.96 96.4% 0+0k 0+0io 0pf+0w