Sun Oct 9 13:06:52 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 Sun Oct 9 2011 at 13:06:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 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: 0.7355676 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): 0.6899999 48.92900 ymin,ymax (A): -27.05000 21.34800 zmin,zma (A): 39.55900 87.35300 x,y,z range (A): 48.23900 48.39800 47.79400 scale (grids/A): 0.7355676 object centre (A): 24.80950 -2.851001 63.45600 number of atom coordinates read : 2567 total number of charged atoms : 2452 net assigned charge : -0.4999730 assigned positive charge : 396.6797 centred at (gu) : 89.36591 89.62270 91.34988 assigned negative charge : -397.1803 centred at (gu) : 89.21939 89.63522 91.30573 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 9572 nv = 96 ne = 84 npr = 51438 no. pairs analyzed = 51438 no. exposed pairs = 3215 no. arc points = 22003 no. surface atoms = 1080 nbur = 1487 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 692 mr = 5548 m= 4 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 4579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1905 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 10407 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5197645E-08 5.6117241E-08 midg,1,midg; midg,igrid,midg 7.4431945E-09 -2.0368622E-08 1,midg,midg; igrid,midg,midg -2.0144761E-07 1.4025605E-07 gauss-seidel spectral radius is 0.9904110 estimated iterations to convergence 83 setup time was (sec) 0.4200000 now iterating at: 13:06:53 rms-change max change #iterations 0.2667536 34.13162 at 10iterations 3.6044776E-02 4.415302 at 20iterations 4.9611493E-03 0.5988426 at 30iterations 7.6972088E-04 8.7924957E-02 at 40iterations 1.6086873E-04 1.7805099E-02 at 50iterations finished qdiffx linear iterations at : 13:06:55 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.6086873E-04 1.7805099E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 13:06:56 3.455u 0.176s 0:04.05 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 Sun Oct 9 2011 at 13:06:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 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: 2.206703 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): 0.6899999 48.92900 ymin,ymax (A): -27.05000 21.34800 zmin,zma (A): 39.55900 87.35300 x,y,z range (A): 48.23900 48.39800 47.79400 scale (grids/A): 2.206703 object centre (A): 24.80950 -2.851001 63.45600 number of atom coordinates read : 2567 total number of charged atoms : 2452 net assigned charge : -0.4999730 assigned positive charge : 396.6797 centred at (gu) : 88.09689 88.86736 94.04929 assigned negative charge : -397.1803 centred at (gu) : 87.65775 88.90539 93.91676 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 100900 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22003 grid for indexing accessible points = 1.400000 m= 41815 mr = 71598 m= 8615 mr = 32235 m= 827 mr = 5829 m= 22 mr = 425 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 42092 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 19536 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) : 0.7355676 object centre at (A) : 24.80950 -2.851001 63.45600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6956599E-02 1.3153368E-02 midg,1,midg; midg,igrid,midg -7.1013480E-02 -4.9479168E-02 1,midg,midg; igrid,midg,midg -6.0537837E-02 1.8900605E-02 gauss-seidel spectral radius is 0.9989551 estimated iterations to convergence 245 setup time was (sec) 0.7400000 now iterating at: 13:06:57 rms-change max change #iterations 5.714601 219.2227 at 10iterations 2.927217 84.79997 at 20iterations 1.512073 42.98770 at 30iterations 0.7785473 19.69859 at 40iterations 0.4011851 10.49356 at 50iterations 0.2067897 6.243149 at 60iterations 0.1066943 2.976671 at 70iterations 5.5051230E-02 1.385139 at 80iterations 2.8449610E-02 0.7211189 at 90iterations 1.4671306E-02 0.4169216 at 100iterations 7.5932373E-03 0.2035475 at 110iterations 3.9429320E-03 0.1038871 at 120iterations finished qdiffx linear iterations at : 13:07:04 total time elapsed so far: 8.060000 # loops : 120 mean,max change (kT/e) : 3.9429320E-03 0.1038871 energy calculations done at 8.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 13:07:05 8.206u 0.202s 0:08.73 96.2% 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 Sun Oct 9 2011 at 13:07:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 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: 3.310054 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): 0.6899999 48.92900 ymin,ymax (A): -27.05000 21.34800 zmin,zma (A): 39.55900 87.35300 x,y,z range (A): 48.23900 48.39800 47.79400 scale (grids/A): 3.310054 object centre (A): 24.80950 -2.851001 63.45600 number of atom coordinates read : 2567 total number of charged atoms : 2452 net assigned charge : -0.4999730 assigned positive charge : 396.6797 centred at (gu) : 87.14511 88.30093 96.07376 assigned negative charge : -397.1803 centred at (gu) : 86.48654 88.35802 95.87497 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 232366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22003 grid for indexing accessible points = 1.400000 m= 128509 mr = 172243 m= 54483 mr = 107388 m= 16343 mr = 45454 m= 3328 mr = 12825 m= 407 mr = 2412 m= 24 mr = 239 m= 0 mr = 6 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 94893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 19616 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) : 2.206703 object centre at (A) : 24.80950 -2.851001 63.45600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3681592 -0.1963387 midg,1,midg; midg,igrid,midg -1.434969 -0.7731031 1,midg,midg; igrid,midg,midg -0.7208275 7.2074719E-02 gauss-seidel spectral radius is 0.9993340 estimated iterations to convergence 306 setup time was (sec) 1.810000 now iterating at: 13:07:07 rms-change max change #iterations 12.44676 401.1001 at 10iterations 7.497797 147.1383 at 20iterations 4.500336 86.99686 at 30iterations 2.701213 44.34392 at 40iterations 1.614385 24.59954 at 50iterations 0.9636923 15.66033 at 60iterations 0.5740234 9.247597 at 70iterations 0.3424173 5.278679 at 80iterations 0.2036899 3.065928 at 90iterations 0.1209133 1.808084 at 100iterations 7.2022319E-02 1.090382 at 110iterations 4.2691875E-02 0.6546593 at 120iterations 2.5511159E-02 0.3667550 at 130iterations 1.5207374E-02 0.2274799 at 140iterations 9.1207111E-03 0.1493139 at 150iterations 5.5289133E-03 8.3229065E-02 at 160iterations 3.4100055E-03 5.7977676E-02 at 170iterations 2.1485558E-03 4.3107986E-02 at 180iterations finished qdiffx linear iterations at : 13:07:19 total time elapsed so far: 13.66000 # loops : 180 mean,max change (kT/e) : 2.1485558E-03 4.3107986E-02 energy calculations done at 13.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.80000 DelPhi exited at 13:07:19 13.797u 0.229s 0:14.29 98.0% 0+0k 0+0io 0pf+0w