Tue Oct 11 06:01:14 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 06:01:14 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 0.7066437 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): 25.62900 71.97900 ymin,ymax (A): -18.78300 31.59600 zmin,zma (A): 3.948000 46.28300 x,y,z range (A): 46.35000 50.37900 42.33500 scale (grids/A): 0.7066437 object centre (A): 48.80400 6.406501 25.11550 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 89.24996 90.17947 90.36251 assigned negative charge : -317.2741 centred at (gu) : 89.37823 90.13061 90.44515 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7203 nv = 96 ne = 84 npr = 42545 no. pairs analyzed = 42545 no. exposed pairs = 2573 no. arc points = 17500 no. surface atoms = 875 nbur = 1443 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 497 mr = 4221 m= 4 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1602 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7975 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7595062E-08 1.2963937E-08 midg,1,midg; midg,igrid,midg 2.8280475E-08 8.0178445E-08 1,midg,midg; igrid,midg,midg 1.3430130E-07 -8.8230312E-09 gauss-seidel spectral radius is 0.9895637 estimated iterations to convergence 80 setup time was (sec) 0.5200000 now iterating at: 06:01:15 rms-change max change #iterations 0.1999416 29.18356 at 10iterations 2.5210893E-02 3.116886 at 20iterations 3.2783619E-03 0.4093857 at 30iterations 5.4017908E-04 7.0045471E-02 at 40iterations 1.3623206E-04 1.6110420E-02 at 50iterations finished qdiffx linear iterations at : 06:01:18 total time elapsed so far: 4.220000 # loops : 50 mean,max change (kT/e) : 1.3623206E-04 1.6110420E-02 energy calculations done at 4.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.390000 DelPhi exited at 06:01:19 4.397u 0.405s 0:05.45 87.8% 0+0k 0+0io 6pf+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 06:01:19 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 2.119931 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): 25.62900 71.97900 ymin,ymax (A): -18.78300 31.59600 zmin,zma (A): 3.948000 46.28300 x,y,z range (A): 46.35000 50.37900 42.33500 scale (grids/A): 2.119931 object centre (A): 48.80400 6.406501 25.11550 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 87.74978 90.53832 91.08758 assigned negative charge : -317.2741 centred at (gu) : 88.13461 90.39195 91.33560 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76196 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17500 grid for indexing accessible points = 1.400000 m= 31468 mr = 54555 m= 6071 mr = 24181 m= 600 mr = 4149 m= 20 mr = 331 m= 0 mr = 6 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 31133 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 15829 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) : 0.7066437 object centre at (A) : 48.80400 6.406501 25.11550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0973131E-02 2.8052555E-02 midg,1,midg; midg,igrid,midg 4.5636281E-02 2.6121041E-02 1,midg,midg; igrid,midg,midg 4.4284422E-02 -4.6210218E-02 gauss-seidel spectral radius is 0.9988312 estimated iterations to convergence 232 setup time was (sec) 0.9600000 now iterating at: 06:01:21 rms-change max change #iterations 4.608721 224.1712 at 10iterations 2.279671 80.16763 at 20iterations 1.130197 37.53630 at 30iterations 0.5614554 16.00079 at 40iterations 0.2798268 11.11492 at 50iterations 0.1386421 4.479866 at 60iterations 6.8944000E-02 2.088140 at 70iterations 3.4240969E-02 1.168495 at 80iterations 1.7137270E-02 0.4715805 at 90iterations 8.5518286E-03 0.2513105 at 100iterations 4.2921356E-03 0.1257205 at 110iterations 2.1994179E-03 6.7523956E-02 at 120iterations finished qdiffx linear iterations at : 06:01:30 total time elapsed so far: 10.67000 # loops : 120 mean,max change (kT/e) : 2.1994179E-03 6.7523956E-02 energy calculations done at 10.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.84000 DelPhi exited at 06:01:31 10.847u 0.442s 0:11.76 95.9% 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 Tue Oct 11 2011 at 06:01:31 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 3.179897 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): 25.62900 71.97900 ymin,ymax (A): -18.78300 31.59600 zmin,zma (A): 3.948000 46.28300 x,y,z range (A): 46.35000 50.37900 42.33500 scale (grids/A): 3.179897 object centre (A): 48.80400 6.406501 25.11550 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 86.62462 90.80762 91.63127 assigned negative charge : -317.2741 centred at (gu) : 87.20198 90.58803 92.00343 start vw surface at 0.1000000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 175769 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17500 grid for indexing accessible points = 1.400000 m= 97540 mr = 131422 m= 39893 mr = 81736 m= 11579 mr = 33066 m= 2396 mr = 9164 m= 324 mr = 1733 m= 29 mr = 221 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.990000 number of dielectric boundary points 70172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 15952 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) : 2.119931 object centre at (A) : 48.80400 6.406501 25.11550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1236218 0.2398146 midg,1,midg; midg,igrid,midg 0.3498400 0.1051149 1,midg,midg; igrid,midg,midg 0.4358000 -0.5772664 gauss-seidel spectral radius is 0.9992967 estimated iterations to convergence 297 setup time was (sec) 2.310000 now iterating at: 06:01:34 rms-change max change #iterations 10.26481 325.7181 at 10iterations 6.072042 139.9532 at 20iterations 3.597711 122.6848 at 30iterations 2.122528 40.48224 at 40iterations 1.251151 29.28333 at 50iterations 0.7353283 17.14611 at 60iterations 0.4315165 7.996065 at 70iterations 0.2536022 4.761410 at 80iterations 0.1487713 2.577202 at 90iterations 8.7270774E-02 1.656189 at 100iterations 5.1231742E-02 0.8924141 at 110iterations 3.0124905E-02 0.5332012 at 120iterations 1.7847331E-02 0.3276291 at 130iterations 1.0663968E-02 0.1899490 at 140iterations 6.4996639E-03 0.1490250 at 150iterations 4.0587075E-03 9.2926025E-02 at 160iterations 2.6591921E-03 4.9652100E-02 at 170iterations 1.8340898E-03 3.4950256E-02 at 180iterations finished qdiffx linear iterations at : 06:01:50 total time elapsed so far: 18.22000 # loops : 180 mean,max change (kT/e) : 1.8340898E-03 3.4950256E-02 energy calculations done at 18.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.39000 DelPhi exited at 06:01:50 18.393u 0.495s 0:19.28 97.9% 0+0k 0+0io 0pf+0w