Sat Oct 15 11:52:39 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 15 2011 at 11:52:39 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2324 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6664420 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): -25.59300 25.86200 ymin,ymax (A): 7.723000 51.09200 zmin,zma (A): -13.77900 39.63900 x,y,z range (A): 51.45500 43.36900 53.41800 scale (grids/A): 0.6664420 object centre (A): 0.1344995 29.40750 12.93000 number of atom coordinates read : 2324 total number of charged atoms : 2181 net assigned charge : 11.00002 assigned positive charge : 336.7263 centred at (gu) : 89.83549 90.28819 92.06200 assigned negative charge : -325.7271 centred at (gu) : 89.86446 90.22356 92.05693 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7136 nv = 96 ne = 84 npr = 46712 no. pairs analyzed = 46712 no. exposed pairs = 3004 no. arc points = 21736 no. surface atoms = 1015 nbur = 1309 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 452 mr = 3823 m= 3 mr = 57 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 0.1900000 number of dielectric boundary points 3711 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2024 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8113 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1381693E-08 5.1520875E-08 midg,1,midg; midg,igrid,midg 1.9258632E-08 4.8245255E-08 1,midg,midg; igrid,midg,midg 3.9933823E-08 2.6492264E-08 gauss-seidel spectral radius is 0.9883128 estimated iterations to convergence 75 setup time was (sec) 0.3800000 now iterating at: 11:52:40 rms-change max change #iterations 0.1645344 24.41444 at 10iterations 1.7719397E-02 2.310566 at 20iterations 2.0049762E-03 0.2738323 at 30iterations 3.3457478E-04 5.9967041E-02 at 40iterations 1.0531285E-04 1.9870758E-02 at 50iterations finished qdiffx linear iterations at : 11:52:43 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.0531285E-04 1.9870758E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 11:52:43 3.448u 0.190s 0:04.05 89.6% 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 Sat Oct 15 2011 at 11:52:43 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2324 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.999326 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): -25.59300 25.86200 ymin,ymax (A): 7.723000 51.09200 zmin,zma (A): -13.77900 39.63900 x,y,z range (A): 51.45500 43.36900 53.41800 scale (grids/A): 1.999326 object centre (A): 0.1344995 29.40750 12.93000 number of atom coordinates read : 2324 total number of charged atoms : 2181 net assigned charge : 11.00002 assigned positive charge : 336.7263 centred at (gu) : 89.50626 90.86424 96.18565 assigned negative charge : -325.7271 centred at (gu) : 89.59357 90.67052 96.17091 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21736 grid for indexing accessible points = 1.400000 m= 28941 mr = 52204 m= 5291 mr = 21312 m= 416 mr = 3307 m= 5 mr = 179 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 34189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 17252 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) : 0.6664420 object centre at (A) : 0.1344995 29.40750 12.93000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9183793E-02 3.5349902E-02 midg,1,midg; midg,igrid,midg 1.6406933E-03 2.9248063E-02 1,midg,midg; igrid,midg,midg 5.3814948E-02 5.2641351E-02 gauss-seidel spectral radius is 0.9987375 estimated iterations to convergence 223 setup time was (sec) 0.6400000 now iterating at: 11:52:44 rms-change max change #iterations 4.263440 212.3585 at 10iterations 2.053937 85.08489 at 20iterations 0.9872804 33.54069 at 30iterations 0.4753014 16.45226 at 40iterations 0.2294254 6.771038 at 50iterations 0.1108446 3.444161 at 60iterations 5.3449940E-02 1.660885 at 70iterations 2.5827158E-02 0.7567673 at 80iterations 1.2453248E-02 0.3933983 at 90iterations 6.0093650E-03 0.1839436 at 100iterations 2.9415849E-03 8.7176085E-02 at 110iterations 1.4519430E-03 4.7405243E-02 at 120iterations finished qdiffx linear iterations at : 11:52:52 total time elapsed so far: 8.150000 # loops : 120 mean,max change (kT/e) : 1.4519430E-03 4.7405243E-02 energy calculations done at 8.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.280000 DelPhi exited at 11:52:52 8.286u 0.248s 0:08.84 96.3% 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 15 2011 at 11:52:52 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2324 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.998989 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): -25.59300 25.86200 ymin,ymax (A): 7.723000 51.09200 zmin,zma (A): -13.77900 39.63900 x,y,z range (A): 51.45500 43.36900 53.41800 scale (grids/A): 2.998989 object centre (A): 0.1344995 29.40750 12.93000 number of atom coordinates read : 2324 total number of charged atoms : 2181 net assigned charge : 11.00002 assigned positive charge : 336.7263 centred at (gu) : 89.25932 91.29621 99.27835 assigned negative charge : -325.7271 centred at (gu) : 89.39047 91.00576 99.25648 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 176561 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21736 grid for indexing accessible points = 1.400000 m= 91214 mr = 126365 m= 35743 mr = 74352 m= 9774 mr = 28800 m= 1655 mr = 7227 m= 131 mr = 1161 m= 7 mr = 60 m= 0 mr = 2 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 77118 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 17447 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) : 1.999326 object centre at (A) : 0.1344995 29.40750 12.93000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6279385 0.3991587 midg,1,midg; midg,igrid,midg -3.1264599E-02 0.2576099 1,midg,midg; igrid,midg,midg 0.5283665 0.4934285 gauss-seidel spectral radius is 0.9992915 estimated iterations to convergence 296 setup time was (sec) 1.320000 now iterating at: 11:52:54 rms-change max change #iterations 9.899748 394.6124 at 10iterations 5.886256 143.5216 at 20iterations 3.490012 76.67532 at 30iterations 2.061497 40.46520 at 40iterations 1.211822 28.27023 at 50iterations 0.7119792 14.60948 at 60iterations 0.4167585 7.465814 at 70iterations 0.2438944 4.628952 at 80iterations 0.1428067 2.521879 at 90iterations 8.3624072E-02 1.601860 at 100iterations 4.8782758E-02 1.025146 at 110iterations 2.8469669E-02 0.5461642 at 120iterations 1.6665136E-02 0.2919078 at 130iterations 9.7443108E-03 0.1751895 at 140iterations 5.7332511E-03 0.1096144 at 150iterations 3.3787915E-03 6.4319611E-02 at 160iterations 2.0220699E-03 4.1408539E-02 at 170iterations 1.2456530E-03 2.9500484E-02 at 180iterations finished qdiffx linear iterations at : 11:53:13 total time elapsed so far: 14.64000 # loops : 180 mean,max change (kT/e) : 1.2456530E-03 2.9500484E-02 energy calculations done at 14.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.76000 DelPhi exited at 11:53:14 14.766u 0.304s 0:21.76 69.2% 0+0k 0+0io 0pf+0w