Mon Oct 10 17:01:53 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 Mon Oct 10 2011 at 17:01:54 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2772 !!! WARNING: HIT 107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6264738 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): 14.00900 70.83500 ymin,ymax (A): 35.63600 82.60000 zmin,zma (A): 61.88100 117.0820 x,y,z range (A): 56.82600 46.96400 55.20100 scale (grids/A): 0.6264738 object centre (A): 42.42200 59.11800 89.48150 number of atom coordinates read : 2772 total number of charged atoms : 2632 net assigned charge : -3.485977 assigned positive charge : 416.3152 centred at (gu) : 89.02472 89.51702 88.89377 assigned negative charge : -419.8022 centred at (gu) : 88.97744 89.44170 88.81120 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7346 nv = 96 ne = 84 npr = 55586 no. pairs analyzed = 55586 no. exposed pairs = 3657 no. arc points = 25723 no. surface atoms = 1241 nbur = 1531 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 327 mr = 3816 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.2000000 number of dielectric boundary points 3831 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2585 ## 266 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8971 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3305105E-08 2.9699014E-09 midg,1,midg; midg,igrid,midg -1.0884228E-08 2.8763059E-09 1,midg,midg; igrid,midg,midg -9.0767873E-09 6.3868488E-10 gauss-seidel spectral radius is 0.9868255 estimated iterations to convergence 71 setup time was (sec) 0.3900000 now iterating at: 17:01:54 rms-change max change #iterations 0.1359643 18.86993 at 10iterations 1.2747088E-02 2.102661 at 20iterations 1.2057527E-03 0.1710510 at 30iterations 1.1248072E-04 1.4112473E-02 at 40iterations 1.0647652E-05 1.5573502E-03 at 50iterations finished qdiffx linear iterations at : 17:01:57 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 1.0647652E-05 1.5573502E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 17:01:59 3.515u 0.213s 0:05.04 73.8% 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 Mon Oct 10 2011 at 17:01:59 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2772 !!! WARNING: HIT 107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.879421 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): 14.00900 70.83500 ymin,ymax (A): 35.63600 82.60000 zmin,zma (A): 61.88100 117.0820 x,y,z range (A): 56.82600 46.96400 55.20100 scale (grids/A): 1.879421 object centre (A): 42.42200 59.11800 89.48150 number of atom coordinates read : 2772 total number of charged atoms : 2632 net assigned charge : -3.485977 assigned positive charge : 416.3152 centred at (gu) : 87.07339 88.55068 86.68040 assigned negative charge : -419.8022 centred at (gu) : 86.93200 88.32487 86.43333 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79976 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25723 grid for indexing accessible points = 1.400000 m= 26735 mr = 54279 m= 3599 mr = 18832 m= 175 mr = 1960 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1537 time to turn everything in is 0.3900000 number of dielectric boundary points 35369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 184 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20671 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) : 0.6264738 object centre at (A) : 42.42200 59.11800 89.48150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3136781E-04 1.5869712E-02 midg,1,midg; midg,igrid,midg -1.7732682E-02 -4.1529583E-03 1,midg,midg; igrid,midg,midg -5.1531680E-02 2.1011250E-02 gauss-seidel spectral radius is 0.9986228 estimated iterations to convergence 214 setup time was (sec) 0.6200000 now iterating at: 17:02:00 rms-change max change #iterations 4.325294 189.4730 at 10iterations 2.008850 66.94655 at 20iterations 0.9374801 28.58775 at 30iterations 0.4366844 15.15714 at 40iterations 0.2031238 6.156587 at 50iterations 9.5045254E-02 3.049235 at 60iterations 4.4256777E-02 1.292526 at 70iterations 2.0653848E-02 0.6906834 at 80iterations 9.6448334E-03 0.3324623 at 90iterations 4.4988208E-03 0.1353426 at 100iterations 2.1006791E-03 6.8771362E-02 at 110iterations 9.7705808E-04 3.4086704E-02 at 120iterations finished qdiffx linear iterations at : 17:02:07 total time elapsed so far: 8.090000 # loops : 120 mean,max change (kT/e) : 9.7705808E-04 3.4086704E-02 energy calculations done at 8.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 17:02:08 8.229u 0.219s 0:09.15 92.1% 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 17:02:08 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2772 !!! WARNING: HIT 107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.819132 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): 14.00900 70.83500 ymin,ymax (A): 35.63600 82.60000 zmin,zma (A): 61.88100 117.0820 x,y,z range (A): 56.82600 46.96400 55.20100 scale (grids/A): 2.819132 object centre (A): 42.42200 59.11800 89.48150 number of atom coordinates read : 2772 total number of charged atoms : 2632 net assigned charge : -3.485977 assigned positive charge : 416.3152 centred at (gu) : 85.60985 87.82577 85.02061 assigned negative charge : -419.8022 centred at (gu) : 85.39787 87.48711 84.64989 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 185415 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25723 grid for indexing accessible points = 1.400000 m= 88698 mr = 132470 m= 29296 mr = 70922 m= 6148 mr = 22556 m= 727 mr = 4302 m= 30 mr = 405 m= 0 mr = 8 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 5287 time to turn everything in is 1.010000 number of dielectric boundary points 79651 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 21051 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) : 1.879421 object centre at (A) : 42.42200 59.11800 89.48150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2143238 0.1476294 midg,1,midg; midg,igrid,midg -0.1694027 -8.1549205E-02 1,midg,midg; igrid,midg,midg -0.6673755 0.2332552 gauss-seidel spectral radius is 0.9992747 estimated iterations to convergence 293 setup time was (sec) 1.270000 now iterating at: 17:02:09 rms-change max change #iterations 10.42454 388.3603 at 10iterations 6.204817 151.7592 at 20iterations 3.658528 79.73016 at 30iterations 2.142973 47.29351 at 40iterations 1.253290 27.02003 at 50iterations 0.7303930 16.48709 at 60iterations 0.4259153 9.336475 at 70iterations 0.2468814 5.638026 at 80iterations 0.1434984 2.865059 at 90iterations 8.2945727E-02 1.698563 at 100iterations 4.8027232E-02 0.9422073 at 110iterations 2.7811132E-02 0.5245094 at 120iterations 1.6074155E-02 0.3147020 at 130iterations 9.2986617E-03 0.1687241 at 140iterations 5.3637875E-03 0.1052594 at 150iterations 3.1061654E-03 6.0220242E-02 at 160iterations 1.7921682E-03 3.5914421E-02 at 170iterations 1.0388176E-03 2.1301270E-02 at 180iterations finished qdiffx linear iterations at : 17:02:21 total time elapsed so far: 13.33000 # loops : 180 mean,max change (kT/e) : 1.0388176E-03 2.1301270E-02 energy calculations done at 13.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.46000 DelPhi exited at 17:02:22 13.461u 0.222s 0:14.01 97.6% 0+0k 0+0io 0pf+0w