Tue Oct 11 03:27:58 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 03:27:58 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 = 3122 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: 0.6144817 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): -13.64200 44.29300 ymin,ymax (A): -1.110000 55.17000 zmin,zma (A): 33.54900 89.67000 x,y,z range (A): 57.93500 56.28000 56.12100 scale (grids/A): 0.6144817 object centre (A): 15.32550 27.03000 61.60950 number of atom coordinates read : 3122 total number of charged atoms : 2966 net assigned charge : -0.4999940 assigned positive charge : 470.5892 centred at (gu) : 89.53697 90.12005 91.35538 assigned negative charge : -471.0903 centred at (gu) : 89.59148 90.22477 91.13097 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7970 nv = 96 ne = 84 npr = 60964 no. pairs analyzed = 60964 no. exposed pairs = 4323 no. arc points = 29858 no. surface atoms = 1462 nbur = 1660 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 4019 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2917 ## 284 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9680 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2056369E-08 1.9685331E-08 midg,1,midg; midg,igrid,midg 6.3623564E-09 -8.0415736E-09 1,midg,midg; igrid,midg,midg 3.5074399E-09 -3.8925507E-09 gauss-seidel spectral radius is 0.9863401 estimated iterations to convergence 70 setup time was (sec) 0.4200000 now iterating at: 03:27:59 rms-change max change #iterations 0.1316735 17.65146 at 10iterations 1.1657655E-02 1.883513 at 20iterations 1.0619567E-03 0.1584320 at 30iterations 9.5787618E-05 1.1672974E-02 at 40iterations 9.0393332E-06 1.3713837E-03 at 50iterations finished qdiffx linear iterations at : 03:28:02 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 9.0393332E-06 1.3713837E-03 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 03:28:02 3.439u 0.171s 0:04.05 88.8% 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 03:28:02 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 = 3122 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: 1.843445 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): -13.64200 44.29300 ymin,ymax (A): -1.110000 55.17000 zmin,zma (A): 33.54900 89.67000 x,y,z range (A): 57.93500 56.28000 56.12100 scale (grids/A): 1.843445 object centre (A): 15.32550 27.03000 61.60950 number of atom coordinates read : 3122 total number of charged atoms : 2966 net assigned charge : -0.4999940 assigned positive charge : 470.5892 centred at (gu) : 88.61039 90.35941 94.06537 assigned negative charge : -471.0903 centred at (gu) : 88.77431 90.67406 93.39249 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 86118 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29858 grid for indexing accessible points = 1.400000 m= 28932 mr = 57489 m= 3683 mr = 19716 m= 173 mr = 1905 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 248 time to turn everything in is 0.4100000 number of dielectric boundary points 39759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 23212 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) : 0.6144817 object centre at (A) : 15.32550 27.03000 61.60950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4519600E-02 5.2051194E-02 midg,1,midg; midg,igrid,midg 1.9821227E-02 8.1301508E-03 1,midg,midg; igrid,midg,midg 3.5540867E-03 -2.8554015E-02 gauss-seidel spectral radius is 0.9986075 estimated iterations to convergence 212 setup time was (sec) 0.6400000 now iterating at: 03:28:03 rms-change max change #iterations 4.430800 206.9534 at 10iterations 2.041693 64.17461 at 20iterations 0.9444648 32.58186 at 30iterations 0.4372537 14.50722 at 40iterations 0.2027791 6.054615 at 50iterations 9.4571896E-02 3.063376 at 60iterations 4.3754790E-02 1.451816 at 70iterations 2.0258121E-02 0.6157417 at 80iterations 9.4171837E-03 0.2949138 at 90iterations 4.3707215E-03 0.1449180 at 100iterations 2.0386586E-03 6.4472198E-02 at 110iterations 9.4551092E-04 3.1542301E-02 at 120iterations finished qdiffx linear iterations at : 03:28:10 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 9.4551092E-04 3.1542301E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 03:28:11 7.950u 0.197s 0:08.55 95.2% 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 Tue Oct 11 2011 at 03:28:11 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 = 3122 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: 2.765168 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): -13.64200 44.29300 ymin,ymax (A): -1.110000 55.17000 zmin,zma (A): 33.54900 89.67000 x,y,z range (A): 57.93500 56.28000 56.12100 scale (grids/A): 2.765168 object centre (A): 15.32550 27.03000 61.60950 number of atom coordinates read : 3122 total number of charged atoms : 2966 net assigned charge : -0.4999940 assigned positive charge : 470.5892 centred at (gu) : 87.91544 90.53889 96.09794 assigned negative charge : -471.0903 centred at (gu) : 88.16138 91.01096 95.08861 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 199378 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29858 grid for indexing accessible points = 1.400000 m= 95588 mr = 140348 m= 31047 mr = 75151 m= 6181 mr = 23264 m= 672 mr = 4050 m= 32 mr = 399 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 815 time to turn everything in is 1.080000 number of dielectric boundary points 89677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 23726 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) : 1.843445 object centre at (A) : 15.32550 27.03000 61.60950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6756188 0.3918699 midg,1,midg; midg,igrid,midg 0.1850035 9.2574634E-02 1,midg,midg; igrid,midg,midg 0.1371027 -0.2837967 gauss-seidel spectral radius is 0.9992710 estimated iterations to convergence 292 setup time was (sec) 1.330000 now iterating at: 03:28:13 rms-change max change #iterations 10.75639 308.6884 at 10iterations 6.432364 146.3222 at 20iterations 3.790823 75.32969 at 30iterations 2.223334 47.79549 at 40iterations 1.300409 25.05552 at 50iterations 0.7605317 15.07307 at 60iterations 0.4414438 8.385576 at 70iterations 0.2563324 4.950033 at 80iterations 0.1485454 2.666569 at 90iterations 8.6404547E-02 1.513519 at 100iterations 4.9934685E-02 0.8565235 at 110iterations 2.8864531E-02 0.5131359 at 120iterations 1.6711945E-02 0.3028156 at 130iterations 9.6573401E-03 0.1767139 at 140iterations 5.5877920E-03 9.5894814E-02 at 150iterations 3.2330574E-03 5.4502487E-02 at 160iterations 1.8660453E-03 3.3232212E-02 at 170iterations 1.0798721E-03 1.8864155E-02 at 180iterations finished qdiffx linear iterations at : 03:28:24 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 1.0798721E-03 1.8864155E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 03:28:25 13.161u 0.211s 0:13.78 97.0% 0+0k 0+0io 0pf+0w