Mon Oct 10 09:53:38 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 09:53:38 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 = 2764 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: 0.5802487 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): -16.58700 36.28600 ymin,ymax (A): -64.25800 -4.727000 zmin,zma (A): -4.461000 56.89200 x,y,z range (A): 52.87300 59.53100 61.35300 scale (grids/A): 0.5802487 object centre (A): 9.849500 -34.49250 26.21550 number of atom coordinates read : 2764 total number of charged atoms : 2615 net assigned charge : 2.000011 assigned positive charge : 402.1031 centred at (gu) : 88.76187 89.47246 87.67331 assigned negative charge : -400.1034 centred at (gu) : 88.90125 89.41122 87.54010 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6405 nv = 96 ne = 84 npr = 52965 no. pairs analyzed = 52965 no. exposed pairs = 4309 no. arc points = 31283 no. surface atoms = 1407 nbur = 1357 mkacc time = 0.1500000 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 = 1.484000 m= 298 mr = 2795 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3700000 number of dielectric boundary points 3893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3017 ## 310 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 7943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8851167E-09 1.7875704E-09 midg,1,midg; midg,igrid,midg -8.4464463E-10 1.4870749E-09 1,midg,midg; igrid,midg,midg 4.2892072E-09 -1.7304407E-09 gauss-seidel spectral radius is 0.9846714 estimated iterations to convergence 66 setup time was (sec) 0.7200000 now iterating at: 09:53:39 rms-change max change #iterations 9.0554722E-02 14.87010 at 10iterations 7.1096779E-03 1.213139 at 20iterations 5.4043415E-04 8.1351280E-02 at 30iterations 4.2007316E-05 6.5994263E-03 at 40iterations 3.5126009E-06 5.4168701E-04 at 50iterations finished qdiffx linear iterations at : 09:53:43 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 3.5126009E-06 5.4168701E-04 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 09:53:43 4.468u 0.274s 0:05.16 91.6% 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 Mon Oct 10 2011 at 09:53:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.740746 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): -16.58700 36.28600 ymin,ymax (A): -64.25800 -4.727000 zmin,zma (A): -4.461000 56.89200 x,y,z range (A): 52.87300 59.53100 61.35300 scale (grids/A): 1.740746 object centre (A): 9.849500 -34.49250 26.21550 number of atom coordinates read : 2764 total number of charged atoms : 2615 net assigned charge : 2.000011 assigned positive charge : 402.1031 centred at (gu) : 86.28483 88.41692 83.01984 assigned negative charge : -400.1034 centred at (gu) : 86.70342 88.23322 82.62001 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 67739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31283 grid for indexing accessible points = 1.400000 m= 21861 mr = 41179 m= 2819 mr = 13942 m= 141 mr = 1242 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 243 time to turn everything in is 0.5200000 number of dielectric boundary points 36181 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 267 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 20305 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) : 0.5802487 object centre at (A) : 9.849500 -34.49250 26.21550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3937734E-02 2.1211433E-03 midg,1,midg; midg,igrid,midg 1.6443258E-02 2.9810002E-02 1,midg,midg; igrid,midg,midg 1.8563053E-02 -1.0520776E-03 gauss-seidel spectral radius is 0.9984105 estimated iterations to convergence 199 setup time was (sec) 0.8300000 now iterating at: 09:53:44 rms-change max change #iterations 3.619638 170.1504 at 10iterations 1.589241 61.00941 at 20iterations 0.7014230 31.29640 at 30iterations 0.3105635 10.30900 at 40iterations 0.1359789 4.950409 at 50iterations 6.0221925E-02 2.378334 at 60iterations 2.6485300E-02 0.9406300 at 70iterations 1.1680922E-02 0.4626722 at 80iterations 5.1300679E-03 0.1785698 at 90iterations 2.2676184E-03 0.1056061 at 100iterations 1.0003913E-03 3.5752773E-02 at 110iterations 4.4172214E-04 1.5486717E-02 at 120iterations finished qdiffx linear iterations at : 09:53:53 total time elapsed so far: 9.290000 # loops : 120 mean,max change (kT/e) : 4.4172214E-04 1.5486717E-02 energy calculations done at 9.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.480000 DelPhi exited at 09:53:54 9.481u 0.280s 0:10.16 96.0% 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 09:53:54 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 = 2764 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.611119 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): -16.58700 36.28600 ymin,ymax (A): -64.25800 -4.727000 zmin,zma (A): -4.461000 56.89200 x,y,z range (A): 52.87300 59.53100 61.35300 scale (grids/A): 2.611119 object centre (A): 9.849500 -34.49250 26.21550 number of atom coordinates read : 2764 total number of charged atoms : 2615 net assigned charge : 2.000011 assigned positive charge : 402.1031 centred at (gu) : 84.42732 87.62531 79.52962 assigned negative charge : -400.1034 centred at (gu) : 85.05505 87.34978 78.92986 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 156470 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31283 grid for indexing accessible points = 1.400000 m= 71155 mr = 101870 m= 23564 mr = 52865 m= 4399 mr = 16851 m= 425 mr = 2590 m= 15 mr = 172 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 840 time to turn everything in is 1.310000 number of dielectric boundary points 81680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 20915 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) : 1.740746 object centre at (A) : 9.849500 -34.49250 26.21550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4342186 1.3716627E-02 midg,1,midg; midg,igrid,midg 0.4154325 0.3994578 1,midg,midg; igrid,midg,midg 0.1786476 2.6472280E-02 gauss-seidel spectral radius is 0.9992239 estimated iterations to convergence 283 setup time was (sec) 1.660000 now iterating at: 09:53:55 rms-change max change #iterations 9.273505 352.5173 at 10iterations 5.489556 146.7564 at 20iterations 3.191709 84.87566 at 30iterations 1.847859 46.30268 at 40iterations 1.065557 25.05410 at 50iterations 0.6113696 16.42937 at 60iterations 0.3500418 8.021355 at 70iterations 0.2004464 5.535074 at 80iterations 0.1139910 2.508317 at 90iterations 6.5035902E-02 1.484951 at 100iterations 3.7106629E-02 0.7939825 at 110iterations 2.1087535E-02 0.4753265 at 120iterations 1.1975199E-02 0.3112904 at 130iterations 6.8241744E-03 0.1384163 at 140iterations 3.8612003E-03 8.5388184E-02 at 150iterations 2.1978770E-03 5.0506592E-02 at 160iterations 1.2440756E-03 2.8557777E-02 at 170iterations 7.0537860E-04 1.4664412E-02 at 180iterations finished qdiffx linear iterations at : 09:54:09 total time elapsed so far: 15.28000 # loops : 180 mean,max change (kT/e) : 7.0537860E-04 1.4664412E-02 energy calculations done at 15.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.47000 DelPhi exited at 09:54:10 15.469u 0.287s 0:16.01 98.3% 0+0k 0+0io 0pf+0w