Sat Oct 8 23:32:35 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 8 2011 at 23:32:35 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2390 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6348867 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): 80.70200 122.8590 ymin,ymax (A): 65.73300 121.8060 zmin,zma (A): 54.93100 108.3570 x,y,z range (A): 42.15701 56.07300 53.42600 scale (grids/A): 0.6348867 object centre (A): 101.7805 93.76950 81.64400 number of atom coordinates read : 2390 total number of charged atoms : 2255 net assigned charge : 11.51402 assigned positive charge : 351.3962 centred at (gu) : 91.04036 89.38335 89.43089 assigned negative charge : -339.8831 centred at (gu) : 90.95351 89.41597 89.41422 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6649 nv = 96 ne = 84 npr = 47872 no. pairs analyzed = 47872 no. exposed pairs = 3059 no. arc points = 21998 no. surface atoms = 1029 nbur = 1361 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 416 mr = 3520 m= 3 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3506 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2182 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7855 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4464602E-08 1.4044407E-08 midg,1,midg; midg,igrid,midg 1.9608759E-08 1.0080768E-08 1,midg,midg; igrid,midg,midg 5.3692037E-09 2.7425758E-08 gauss-seidel spectral radius is 0.9871380 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 23:32:35 rms-change max change #iterations 0.1292930 20.53309 at 10iterations 1.2491651E-02 2.157051 at 20iterations 1.4225442E-03 0.2131653 at 30iterations 2.7113277E-04 4.6669960E-02 at 40iterations 8.5405562E-05 1.4535904E-02 at 50iterations finished qdiffx linear iterations at : 23:32:38 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 8.5405562E-05 1.4535904E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 23:32:39 3.446u 0.197s 0:04.04 89.8% 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 8 2011 at 23:32:39 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2390 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.904660 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): 80.70200 122.8590 ymin,ymax (A): 65.73300 121.8060 zmin,zma (A): 54.93100 108.3570 x,y,z range (A): 42.15701 56.07300 53.42600 scale (grids/A): 1.904660 object centre (A): 101.7805 93.76950 81.64400 number of atom coordinates read : 2390 total number of charged atoms : 2255 net assigned charge : 11.51402 assigned positive charge : 351.3962 centred at (gu) : 93.12077 88.14977 88.29250 assigned negative charge : -339.8831 centred at (gu) : 92.86064 88.24810 88.24263 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70954 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21998 grid for indexing accessible points = 1.400000 m= 26810 mr = 48080 m= 4723 mr = 19711 m= 332 mr = 2924 m= 6 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 557 time to turn everything in is 0.3500000 number of dielectric boundary points 31963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17759 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) : 0.6348867 object centre at (A) : 101.7805 93.76950 81.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8926070E-02 3.5693843E-02 midg,1,midg; midg,igrid,midg 3.6270116E-02 5.3696498E-02 1,midg,midg; igrid,midg,midg 2.8213435E-03 3.4840140E-02 gauss-seidel spectral radius is 0.9986240 estimated iterations to convergence 214 setup time was (sec) 0.5700000 now iterating at: 23:32:40 rms-change max change #iterations 3.964117 181.1829 at 10iterations 1.850055 71.44121 at 20iterations 0.8645712 29.53389 at 30iterations 0.4009449 12.63231 at 40iterations 0.1870265 6.774906 at 50iterations 8.7152645E-02 2.742715 at 60iterations 4.0852875E-02 1.304469 at 70iterations 1.9112904E-02 0.6068292 at 80iterations 8.9718420E-03 0.2880774 at 90iterations 4.2144223E-03 0.1363182 at 100iterations 2.0085569E-03 7.1014404E-02 at 110iterations 9.8299549E-04 3.7895203E-02 at 120iterations finished qdiffx linear iterations at : 23:32:47 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 9.8299549E-04 3.7895203E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 23:32:47 7.738u 0.218s 0:08.27 96.0% 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 8 2011 at 23:32:47 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2390 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.856990 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): 80.70200 122.8590 ymin,ymax (A): 65.73300 121.8060 zmin,zma (A): 54.93100 108.3570 x,y,z range (A): 42.15701 56.07300 53.42600 scale (grids/A): 2.856990 object centre (A): 101.7805 93.76950 81.64400 number of atom coordinates read : 2390 total number of charged atoms : 2255 net assigned charge : 11.51402 assigned positive charge : 351.3962 centred at (gu) : 94.68098 87.22454 87.43860 assigned negative charge : -339.8831 centred at (gu) : 94.29092 87.37222 87.36396 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 163796 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21998 grid for indexing accessible points = 1.400000 m= 84571 mr = 116726 m= 32814 mr = 68657 m= 8730 mr = 26394 m= 1415 mr = 6460 m= 113 mr = 943 m= 4 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 1625 time to turn everything in is 0.9100000 number of dielectric boundary points 72195 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 18040 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) : 1.904660 object centre at (A) : 101.7805 93.76950 81.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4772346 0.3802730 midg,1,midg; midg,igrid,midg 0.3921786 0.6554572 1,midg,midg; igrid,midg,midg 1.7133571E-02 0.3606895 gauss-seidel spectral radius is 0.9992610 estimated iterations to convergence 290 setup time was (sec) 1.140000 now iterating at: 23:32:48 rms-change max change #iterations 9.430330 382.5452 at 10iterations 5.526857 121.9790 at 20iterations 3.219277 67.39122 at 30iterations 1.875781 41.49733 at 40iterations 1.087870 21.75038 at 50iterations 0.6319556 13.72561 at 60iterations 0.3656492 7.326683 at 70iterations 0.2104653 4.027457 at 80iterations 0.1217646 2.483079 at 90iterations 7.0267007E-02 1.343938 at 100iterations 4.0473163E-02 0.7712364 at 110iterations 2.3291985E-02 0.5053463 at 120iterations 1.3457011E-02 0.2719314 at 130iterations 7.7638905E-03 0.1411781 at 140iterations 4.4761030E-03 8.9851379E-02 at 150iterations 2.5786033E-03 5.1112175E-02 at 160iterations 1.4968428E-03 2.9561043E-02 at 170iterations 8.6986995E-04 1.8910408E-02 at 180iterations finished qdiffx linear iterations at : 23:33:01 total time elapsed so far: 12.49000 # loops : 180 mean,max change (kT/e) : 8.6986995E-04 1.8910408E-02 energy calculations done at 12.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 23:33:01 12.624u 1.087s 0:13.98 97.9% 0+0k 0+0io 0pf+0w