Tue Oct 11 03:48:31 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 Tue Oct 11 2011 at 03:48:31 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2895 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6607029 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): -15.41300 34.55300 ymin,ymax (A): 7.001000 55.43000 zmin,zma (A): 25.97200 79.85400 x,y,z range (A): 49.96600 48.42900 53.88200 scale (grids/A): 0.6607029 object centre (A): 9.570002 31.21550 52.91300 number of atom coordinates read : 2895 total number of charged atoms : 2741 net assigned charge : 2.162016 assigned positive charge : 439.0515 centred at (gu) : 89.94187 90.38903 88.97298 assigned negative charge : -436.8902 centred at (gu) : 90.19522 90.27899 88.97356 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8392 nv = 96 ne = 84 npr = 59499 no. pairs analyzed = 59499 no. exposed pairs = 3488 no. arc points = 24221 no. surface atoms = 1173 nbur = 1722 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 461 mr = 4822 m= 0 mr = 69 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2200000 number of dielectric boundary points 3962 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2360 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 10044 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9822308E-09 4.4130246E-09 midg,1,midg; midg,igrid,midg -1.8105132E-08 3.2767907E-08 1,midg,midg; igrid,midg,midg 6.2200712E-08 -5.2782855E-08 gauss-seidel spectral radius is 0.9881486 estimated iterations to convergence 75 setup time was (sec) 0.4000000 now iterating at: 03:48:31 rms-change max change #iterations 0.1748004 22.36739 at 10iterations 1.9353926E-02 2.374529 at 20iterations 2.1375618E-03 0.2619553 at 30iterations 2.5384285E-04 3.2678127E-02 at 40iterations 4.1335934E-05 5.1383972E-03 at 50iterations finished qdiffx linear iterations at : 03:48:34 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 4.1335934E-05 5.1383972E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 03:48:35 3.359u 0.164s 0:03.96 88.6% 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 Tue Oct 11 2011 at 03:48:35 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2895 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.982109 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): -15.41300 34.55300 ymin,ymax (A): 7.001000 55.43000 zmin,zma (A): 25.97200 79.85400 x,y,z range (A): 49.96600 48.42900 53.88200 scale (grids/A): 1.982109 object centre (A): 9.570002 31.21550 52.91300 number of atom coordinates read : 2895 total number of charged atoms : 2741 net assigned charge : 2.162016 assigned positive charge : 439.0515 centred at (gu) : 89.82516 91.16682 86.91856 assigned negative charge : -436.8902 centred at (gu) : 90.58560 90.83665 86.92060 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 90704 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24221 grid for indexing accessible points = 1.400000 m= 34779 mr = 64734 m= 5811 mr = 26367 m= 431 mr = 3819 m= 11 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1194 time to turn everything in is 0.4500000 number of dielectric boundary points 36635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 21633 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) : 0.6607029 object centre at (A) : 9.570002 31.21550 52.91300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0570786E-03 -2.0487968E-02 midg,1,midg; midg,igrid,midg -1.2286805E-02 1.8344568E-02 1,midg,midg; igrid,midg,midg 8.1053421E-02 -1.0710852E-02 gauss-seidel spectral radius is 0.9987622 estimated iterations to convergence 225 setup time was (sec) 0.6600000 now iterating at: 03:48:36 rms-change max change #iterations 4.946010 231.8201 at 10iterations 2.413290 79.20601 at 20iterations 1.168833 33.41204 at 30iterations 0.5702131 16.81543 at 40iterations 0.2779567 9.396381 at 50iterations 0.1346209 3.964444 at 60iterations 6.5712355E-02 1.911306 at 70iterations 3.1965300E-02 0.8854942 at 80iterations 1.5537522E-02 0.4276981 at 90iterations 7.5934702E-03 0.2114563 at 100iterations 3.6951110E-03 0.1004229 at 110iterations 1.8138756E-03 5.1412582E-02 at 120iterations finished qdiffx linear iterations at : 03:48:43 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.8138756E-03 5.1412582E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 03:48:43 7.800u 0.185s 0:08.42 94.7% 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 Tue Oct 11 2011 at 03:48:43 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2895 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.973163 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): -15.41300 34.55300 ymin,ymax (A): 7.001000 55.43000 zmin,zma (A): 25.97200 79.85400 x,y,z range (A): 49.96600 48.42900 53.88200 scale (grids/A): 2.973163 object centre (A): 9.570002 31.21550 52.91300 number of atom coordinates read : 2895 total number of charged atoms : 2741 net assigned charge : 2.162016 assigned positive charge : 439.0515 centred at (gu) : 89.73746 91.75020 85.37764 assigned negative charge : -436.8902 centred at (gu) : 90.87825 91.25504 85.38084 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 209413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24221 grid for indexing accessible points = 1.400000 m= 111502 mr = 155877 m= 41915 mr = 93045 m= 10723 mr = 34279 m= 1806 mr = 8302 m= 138 mr = 1318 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 3945 time to turn everything in is 1.160000 number of dielectric boundary points 82617 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 21924 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) : 1.982109 object centre at (A) : 9.570002 31.21550 52.91300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1120882 -0.2839828 midg,1,midg; midg,igrid,midg -0.1454624 0.2293179 1,midg,midg; igrid,midg,midg 0.6912105 -6.3509554E-02 gauss-seidel spectral radius is 0.9992923 estimated iterations to convergence 297 setup time was (sec) 1.400000 now iterating at: 03:48:45 rms-change max change #iterations 11.26295 505.0036 at 10iterations 6.640873 147.2998 at 20iterations 3.917170 78.65550 at 30iterations 2.295977 44.00058 at 40iterations 1.348459 26.05848 at 50iterations 0.7907793 15.28012 at 60iterations 0.4632614 8.650829 at 70iterations 0.2708764 5.163700 at 80iterations 0.1583008 2.754392 at 90iterations 9.2432469E-02 1.474714 at 100iterations 5.3866871E-02 0.8649826 at 110iterations 3.1543605E-02 0.5404148 at 120iterations 1.8389933E-02 0.3136158 at 130iterations 1.0736887E-02 0.1732836 at 140iterations 6.2789735E-03 0.1014366 at 150iterations 3.6744142E-03 5.8506966E-02 at 160iterations 2.1569824E-03 3.7666321E-02 at 170iterations 1.2714486E-03 1.9866943E-02 at 180iterations finished qdiffx linear iterations at : 03:48:56 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 1.2714486E-03 1.9866943E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.98000 DelPhi exited at 03:48:57 12.984u 0.210s 0:13.48 97.8% 0+0k 0+0io 0pf+0w