Sat Oct 8 11:52:13 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 Sat Oct 8 2011 at 11:52:13 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 = 2477 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6375015 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): -25.02900 30.81400 ymin,ymax (A): -6.087000 39.99200 zmin,zma (A): 8.392000 50.79600 x,y,z range (A): 55.84300 46.07900 42.40400 scale (grids/A): 0.6375015 object centre (A): 2.892500 16.95250 29.59400 number of atom coordinates read : 2477 total number of charged atoms : 2337 net assigned charge : -1.999994 assigned positive charge : 376.0463 centred at (gu) : 89.89867 89.40649 91.09190 assigned negative charge : -378.0467 centred at (gu) : 90.01289 89.28497 91.10557 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6654 nv = 96 ne = 84 npr = 50842 no. pairs analyzed = 50842 no. exposed pairs = 2901 no. arc points = 21287 no. surface atoms = 971 nbur = 1506 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 327 mr = 3656 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3800000 number of dielectric boundary points 3296 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2081 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8000 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.3741359E-10 -5.1084936E-09 midg,1,midg; midg,igrid,midg -1.7812317E-08 8.8642134E-09 1,midg,midg; igrid,midg,midg 9.5681116E-09 -1.4534214E-08 gauss-seidel spectral radius is 0.9872407 estimated iterations to convergence 72 setup time was (sec) 0.7100000 now iterating at: 11:52:14 rms-change max change #iterations 0.1419022 20.98545 at 10iterations 1.3758658E-02 1.935534 at 20iterations 1.3381930E-03 0.1685066 at 30iterations 1.3075490E-04 2.1156311E-02 at 40iterations 1.2958239E-05 2.0408630E-03 at 50iterations finished qdiffx linear iterations at : 11:52:18 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 1.2958239E-05 2.0408630E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.520000 DelPhi exited at 11:52:19 4.523u 0.450s 0:05.30 93.7% 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 Sat Oct 8 2011 at 11:52:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2477 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.912505 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): -25.02900 30.81400 ymin,ymax (A): -6.087000 39.99200 zmin,zma (A): 8.392000 50.79600 x,y,z range (A): 55.84300 46.07900 42.40400 scale (grids/A): 1.912505 object centre (A): 2.892500 16.95250 29.59400 number of atom coordinates read : 2477 total number of charged atoms : 2337 net assigned charge : -1.999994 assigned positive charge : 376.0463 centred at (gu) : 89.69558 88.21918 93.27538 assigned negative charge : -378.0467 centred at (gu) : 90.03854 87.85498 93.31641 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 72282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21287 grid for indexing accessible points = 1.400000 m= 25236 mr = 50353 m= 3986 mr = 18492 m= 275 mr = 2511 m= 7 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1670 time to turn everything in is 0.7500000 number of dielectric boundary points 30320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 18356 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) : 0.6375015 object centre at (A) : 2.892500 16.95250 29.59400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9599750E-03 -1.4704361E-02 midg,1,midg; midg,igrid,midg -1.4285827E-02 4.2807902E-03 1,midg,midg; igrid,midg,midg 1.7500697E-02 -5.0071191E-02 gauss-seidel spectral radius is 0.9986312 estimated iterations to convergence 214 setup time was (sec) 1.090000 now iterating at: 11:52:20 rms-change max change #iterations 4.205499 175.6089 at 10iterations 1.967278 70.13087 at 20iterations 0.9201650 32.20463 at 30iterations 0.4300970 15.41078 at 40iterations 0.1998928 6.256460 at 50iterations 9.3953244E-02 2.968982 at 60iterations 4.3855902E-02 1.499082 at 70iterations 2.0576328E-02 0.6362329 at 80iterations 9.6018445E-03 0.2948263 at 90iterations 4.5080250E-03 0.1429300 at 100iterations 2.1151339E-03 6.4304352E-02 at 110iterations 9.8543416E-04 3.4088135E-02 at 120iterations finished qdiffx linear iterations at : 11:52:30 total time elapsed so far: 10.72000 # loops : 120 mean,max change (kT/e) : 9.8543416E-04 3.4088135E-02 energy calculations done at 10.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.94000 DelPhi exited at 11:52:30 10.941u 0.461s 0:11.71 97.3% 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 Sat Oct 8 2011 at 11:52:30 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 = 2477 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.868757 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): -25.02900 30.81400 ymin,ymax (A): -6.087000 39.99200 zmin,zma (A): 8.392000 50.79600 x,y,z range (A): 55.84300 46.07900 42.40400 scale (grids/A): 2.868757 object centre (A): 2.892500 16.95250 29.59400 number of atom coordinates read : 2477 total number of charged atoms : 2337 net assigned charge : -1.999994 assigned positive charge : 376.0463 centred at (gu) : 89.54325 87.32880 94.91303 assigned negative charge : -378.0467 centred at (gu) : 90.05777 86.78242 94.97468 start vw surface at 0.1600000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 167544 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21287 grid for indexing accessible points = 1.400000 m= 82466 mr = 122330 m= 29193 mr = 67479 m= 7356 mr = 23215 m= 1253 mr = 5552 m= 102 mr = 878 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 5775 time to turn everything in is 1.900000 number of dielectric boundary points 68416 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 18687 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) : 1.912505 object centre at (A) : 2.892500 16.95250 29.59400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9682435E-02 -0.2374484 midg,1,midg; midg,igrid,midg -0.1374069 -7.5762854E-03 1,midg,midg; igrid,midg,midg 0.2348194 -0.8200419 gauss-seidel spectral radius is 0.9992503 estimated iterations to convergence 288 setup time was (sec) 2.260000 now iterating at: 11:52:33 rms-change max change #iterations 9.677374 537.7126 at 10iterations 5.586465 146.8652 at 20iterations 3.200709 58.00974 at 30iterations 1.828342 37.95477 at 40iterations 1.044851 19.81190 at 50iterations 0.5975555 11.39517 at 60iterations 0.3417740 6.291580 at 70iterations 0.1954383 3.596910 at 80iterations 0.1116516 2.128170 at 90iterations 6.3611358E-02 1.132759 at 100iterations 3.6441579E-02 0.6613674 at 110iterations 2.0787105E-02 0.3953872 at 120iterations 1.1880272E-02 0.2198575 at 130iterations 6.7945509E-03 0.1181297 at 140iterations 3.8761720E-03 6.7790985E-02 at 150iterations 2.2161945E-03 3.8879395E-02 at 160iterations 1.2636979E-03 2.3014069E-02 at 170iterations 7.2385091E-04 1.3057709E-02 at 180iterations finished qdiffx linear iterations at : 11:52:48 total time elapsed so far: 17.32000 # loops : 180 mean,max change (kT/e) : 7.2385091E-04 1.3057709E-02 energy calculations done at 17.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.54000 DelPhi exited at 11:52:49 17.548u 0.538s 0:18.37 98.3% 0+0k 0+0io 0pf+0w