Mon Oct 10 16:03:04 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 Mon Oct 10 2011 at 16:03:04 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 = 4800 !!! WARNING: ASP 608 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5400977 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): -19.38700 46.52700 ymin,ymax (A): 8.200999 73.07300 zmin,zma (A): 33.74000 95.33600 x,y,z range (A): 65.91400 64.87200 61.59600 scale (grids/A): 0.5400977 object centre (A): 13.57000 40.63700 64.53799 number of atom coordinates read : 4800 total number of charged atoms : 4641 net assigned charge : 2.000020 assigned positive charge : 722.2164 centred at (gu) : 90.26413 90.95190 89.74718 assigned negative charge : -720.2211 centred at (gu) : 90.23663 90.92290 89.76637 start vw surface at 0.2100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8872 nv = 96 ne = 84 npr = 99268 no. pairs analyzed = 99268 no. exposed pairs = 5806 no. arc points = 39014 no. surface atoms = 1947 nbur = 2853 mkacc time = 0.2300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 341 mr = 4873 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3943 ## 495 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 11829 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7651217E-10 -6.6411363E-11 midg,1,midg; midg,igrid,midg -1.2194781E-10 4.3702170E-10 1,midg,midg; igrid,midg,midg -1.3362420E-10 3.5350758E-10 gauss-seidel spectral radius is 0.9824571 estimated iterations to convergence 62 setup time was (sec) 0.7500000 now iterating at: 16:03:05 rms-change max change #iterations 8.8694133E-02 13.94009 at 10iterations 6.5278634E-03 1.029556 at 20iterations 1.2127260E-03 0.1725578 at 30iterations 4.9630273E-04 6.0890198E-02 at 40iterations 2.3086459E-04 2.9290676E-02 at 50iterations finished qdiffx linear iterations at : 16:03:08 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 2.3086459E-04 2.9290676E-02 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 16:03:08 3.780u 0.200s 0:04.32 92.1% 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 Mon Oct 10 2011 at 16:03:08 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 = 4800 !!! WARNING: ASP 608 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.620293 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): -19.38700 46.52700 ymin,ymax (A): 8.200999 73.07300 zmin,zma (A): 33.74000 95.33600 x,y,z range (A): 65.91400 64.87200 61.59600 scale (grids/A): 1.620293 object centre (A): 13.57000 40.63700 64.53799 number of atom coordinates read : 4800 total number of charged atoms : 4641 net assigned charge : 2.000020 assigned positive charge : 722.2164 centred at (gu) : 90.79078 92.85429 89.24040 assigned negative charge : -720.2211 centred at (gu) : 90.70922 92.76833 89.29876 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 99648 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39014 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31872 mr = 70976 m= 3416 mr = 22194 m= 79 mr = 1688 m= 0 mr = 11 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 682 time to turn everything in is 0.7400000 number of dielectric boundary points 40146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 457 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 35457 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) : 0.5400977 object centre at (A) : 13.57000 40.63700 64.53799 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3962370E-03 1.0787701E-02 midg,1,midg; midg,igrid,midg -4.4310666E-03 -1.2485607E-03 1,midg,midg; igrid,midg,midg -3.4975883E-02 1.0977211E-02 gauss-seidel spectral radius is 0.9983314 estimated iterations to convergence 194 setup time was (sec) 1.050000 now iterating at: 16:03:09 rms-change max change #iterations 4.287673 159.5117 at 10iterations 1.853230 70.36842 at 20iterations 0.8003986 24.31966 at 30iterations 0.3472893 10.94965 at 40iterations 0.1505368 4.456032 at 50iterations 6.5378509E-02 2.021303 at 60iterations 2.8465774E-02 0.8670835 at 70iterations 1.2536473E-02 0.4022856 at 80iterations 5.7075890E-03 0.1947594 at 90iterations 2.7609388E-03 8.1638336E-02 at 100iterations 1.5064672E-03 4.9274445E-02 at 110iterations 9.6759078E-04 2.9105514E-02 at 120iterations finished qdiffx linear iterations at : 16:03:16 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 9.6759078E-04 2.9105514E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.270000 DelPhi exited at 16:03:17 8.272u 0.230s 0:08.79 96.7% 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 Mon Oct 10 2011 at 16:03:17 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 = 4800 !!! WARNING: ASP 608 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.430440 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): -19.38700 46.52700 ymin,ymax (A): 8.200999 73.07300 zmin,zma (A): 33.74000 95.33600 x,y,z range (A): 65.91400 64.87200 61.59600 scale (grids/A): 2.430440 object centre (A): 13.57000 40.63700 64.53799 number of atom coordinates read : 4800 total number of charged atoms : 4641 net assigned charge : 2.000020 assigned positive charge : 722.2164 centred at (gu) : 91.18572 94.28122 88.86021 assigned negative charge : -720.2211 centred at (gu) : 91.06380 94.15240 88.94806 start vw surface at 0.2100000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 232384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39014 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 109667 mr = 173610 m= 32245 mr = 87550 m= 5216 mr = 24475 m= 400 mr = 3482 m= 9 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 2265 time to turn everything in is 1.810000 number of dielectric boundary points 90635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 37082 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) : 1.620293 object centre at (A) : 13.57000 40.63700 64.53799 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0303157E-02 0.1788882 midg,1,midg; midg,igrid,midg -9.6153155E-02 -1.4358144E-02 1,midg,midg; igrid,midg,midg -0.7350684 0.1823172 gauss-seidel spectral radius is 0.9992217 estimated iterations to convergence 283 setup time was (sec) 2.160000 now iterating at: 16:03:19 rms-change max change #iterations 11.16140 274.4156 at 10iterations 6.540667 148.7679 at 20iterations 3.805387 90.69118 at 30iterations 2.205065 47.32817 at 40iterations 1.271801 28.34913 at 50iterations 0.7325402 14.58490 at 60iterations 0.4203008 8.021358 at 70iterations 0.2409116 4.683704 at 80iterations 0.1377952 2.425403 at 90iterations 7.8703560E-02 1.402509 at 100iterations 4.5006610E-02 0.8196836 at 110iterations 2.5706060E-02 0.4279175 at 120iterations 1.4727947E-02 0.2585649 at 130iterations 8.4722601E-03 0.1821761 at 140iterations 4.9242033E-03 9.0301514E-02 at 150iterations 2.9211312E-03 5.0676346E-02 at 160iterations 1.7981442E-03 3.0963898E-02 at 170iterations 1.1742805E-03 1.9788742E-02 at 180iterations finished qdiffx linear iterations at : 16:03:31 total time elapsed so far: 13.58000 # loops : 180 mean,max change (kT/e) : 1.1742805E-03 1.9788742E-02 energy calculations done at 13.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.77000 DelPhi exited at 16:03:31 13.772u 0.237s 0:14.28 98.0% 0+0k 0+0io 0pf+0w