Thu Jan 26 12:31:03 PST 2012 #!/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 Thu Jan 26 2012 at 12:31:03 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 ! Automatically converted by prot2crg.py # of charge parameter records: 944 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 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: 0.6411065 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): -11.37100 37.03100 ymin,ymax (A): -25.82100 22.41900 zmin,zma (A): -10.26600 45.26300 x,y,z range (A): 48.40200 48.24000 55.52900 scale (grids/A): 0.6411065 object centre (A): 12.83000 -1.701000 17.49850 number of atom coordinates read : 2726 total number of charged atoms : 2578 net assigned charge : -0.4999861 assigned positive charge : 412.2798 centred at (gu) : 90.13236 90.36057 91.81730 assigned negative charge : -412.7803 centred at (gu) : 89.90725 90.23335 91.72100 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7374 nv = 96 ne = 84 npr = 56573 no. pairs analyzed = 56573 no. exposed pairs = 3311 no. arc points = 23082 no. surface atoms = 1109 nbur = 1617 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 4175 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2400000 number of dielectric boundary points 3570 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2272 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8986 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.1064676E-09 1.6582058E-08 midg,1,midg; midg,igrid,midg -1.6180204E-08 1.6167320E-08 1,midg,midg; igrid,midg,midg -2.9601942E-08 2.7740954E-08 gauss-seidel spectral radius is 0.9874012 estimated iterations to convergence 73 setup time was (sec) 0.4400000 now iterating at: 12:31:03 rms-change max change #iterations 0.1541773 22.28472 at 10iterations 1.5504525E-02 2.019386 at 20iterations 1.5865794E-03 0.2137527 at 30iterations 1.6121089E-04 2.1936417E-02 at 40iterations 1.8060973E-05 2.6664734E-03 at 50iterations finished qdiffx linear iterations at : 12:31:06 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 1.8060973E-05 2.6664734E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 12:31:07 3.526u 0.190s 0:04.00 92.7% 0+0k 0+45824io 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 Thu Jan 26 2012 at 12:31:07 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 ! Automatically converted by prot2crg.py # of charge parameter records: 944 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 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: 1.923319 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): -11.37100 37.03100 ymin,ymax (A): -25.82100 22.41900 zmin,zma (A): -10.26600 45.26300 x,y,z range (A): 48.40200 48.24000 55.52900 scale (grids/A): 1.923319 object centre (A): 12.83000 -1.701000 17.49850 number of atom coordinates read : 2726 total number of charged atoms : 2578 net assigned charge : -0.4999861 assigned positive charge : 412.2798 centred at (gu) : 90.39651 91.08105 95.45107 assigned negative charge : -412.7803 centred at (gu) : 89.72146 90.69980 95.16262 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80419 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23082 grid for indexing accessible points = 1.400000 m= 29064 mr = 56903 m= 4297 mr = 21627 m= 233 mr = 2637 m= 1 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 572 time to turn everything in is 0.4900000 number of dielectric boundary points 32773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 20297 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) : 0.6411065 object centre at (A) : 12.83000 -1.701000 17.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7219332E-02 -6.0458342E-03 midg,1,midg; midg,igrid,midg -1.4533698E-02 2.1107946E-02 1,midg,midg; igrid,midg,midg -1.1752073E-02 4.4583451E-02 gauss-seidel spectral radius is 0.9986709 estimated iterations to convergence 217 setup time was (sec) 0.7100000 now iterating at: 12:31:08 rms-change max change #iterations 4.522270 193.3946 at 10iterations 2.148224 69.47502 at 20iterations 1.019354 33.58649 at 30iterations 0.4836119 15.73450 at 40iterations 0.2288685 7.156151 at 50iterations 0.1085922 3.302696 at 60iterations 5.1478051E-02 1.572922 at 70iterations 2.4415612E-02 0.7006302 at 80iterations 1.1590726E-02 0.3218002 at 90iterations 5.4877563E-03 0.1751213 at 100iterations 2.6030294E-03 7.9837799E-02 at 110iterations 1.2458042E-03 3.9581299E-02 at 120iterations finished qdiffx linear iterations at : 12:31:15 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 1.2458042E-03 3.9581299E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 12:31:15 8.100u 0.209s 0:08.69 95.5% 0+0k 0+45264io 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 Thu Jan 26 2012 at 12:31:15 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 ! Automatically converted by prot2crg.py # of charge parameter records: 944 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 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: 2.884979 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): -11.37100 37.03100 ymin,ymax (A): -25.82100 22.41900 zmin,zma (A): -10.26600 45.26300 x,y,z range (A): 48.40200 48.24000 55.52900 scale (grids/A): 2.884979 object centre (A): 12.83000 -1.701000 17.49850 number of atom coordinates read : 2726 total number of charged atoms : 2578 net assigned charge : -0.4999861 assigned positive charge : 412.2798 centred at (gu) : 90.59458 91.62148 98.17642 assigned negative charge : -412.7803 centred at (gu) : 89.58227 91.04969 97.74394 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 186188 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23082 grid for indexing accessible points = 1.400000 m= 94901 mr = 137858 m= 33501 mr = 78203 m= 7752 mr = 26887 m= 1090 mr = 5778 m= 52 mr = 761 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 1856 time to turn everything in is 1.310000 number of dielectric boundary points 73980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 20624 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) : 1.923319 object centre at (A) : 12.83000 -1.701000 17.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6072279 0.1848964 midg,1,midg; midg,igrid,midg -0.1600161 0.2577183 1,midg,midg; igrid,midg,midg -7.2168827E-02 0.3778759 gauss-seidel spectral radius is 0.9992659 estimated iterations to convergence 291 setup time was (sec) 1.530000 now iterating at: 12:31:17 rms-change max change #iterations 10.55359 462.6105 at 10iterations 6.179142 132.2154 at 20iterations 3.614138 79.76540 at 30iterations 2.107879 54.78229 at 40iterations 1.225282 25.70156 at 50iterations 0.7110221 14.35853 at 60iterations 0.4115084 7.703142 at 70iterations 0.2385772 4.270905 at 80iterations 0.1376872 2.417942 at 90iterations 7.9777494E-02 1.522419 at 100iterations 4.6032358E-02 0.7898769 at 110iterations 2.6602259E-02 0.4521098 at 120iterations 1.5370344E-02 0.2547455 at 130iterations 8.8693462E-03 0.1586227 at 140iterations 5.1271780E-03 8.8519096E-02 at 150iterations 2.9644419E-03 5.3272247E-02 at 160iterations 1.7118260E-03 3.2661438E-02 at 170iterations 9.9180732E-04 1.8669128E-02 at 180iterations finished qdiffx linear iterations at : 12:31:29 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 9.9180732E-04 1.8669128E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 12:31:29 13.095u 0.226s 0:13.60 97.8% 0+0k 0+45256io 0pf+0w