Mon Oct 10 17:02:37 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+sph2.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 = amb2.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 17:02:37 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2283 !!! WARNING: GLM 55 has a net charge of -0.0940 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: 0.6391611 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): -6.154000 39.56500 ymin,ymax (A): 15.97300 71.67101 zmin,zma (A): -0.7520000 48.13500 x,y,z range (A): 45.71900 55.69801 48.88700 scale (grids/A): 0.6391611 object centre (A): 16.70550 43.82200 23.69150 number of atom coordinates read : 2283 total number of charged atoms : 2205 net assigned charge : -4.093994 assigned positive charge : 337.0143 centred at (gu) : 90.41647 89.67343 88.25629 assigned negative charge : -341.1089 centred at (gu) : 90.46710 89.67403 88.20635 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6316 nv = 96 ne = 84 npr = 46052 no. pairs analyzed = 46052 no. exposed pairs = 2982 no. arc points = 20514 no. surface atoms = 1017 nbur = 1266 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 341 mr = 3379 m= 0 mr = 47 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3231 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1984 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7637 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5536552E-08 -5.7287519E-10 midg,1,midg; midg,igrid,midg -6.0084702E-09 -5.3616453E-09 1,midg,midg; igrid,midg,midg -6.1729383E-10 -1.1756359E-08 gauss-seidel spectral radius is 0.9872937 estimated iterations to convergence 73 setup time was (sec) 0.5900000 now iterating at: 17:02:38 rms-change max change #iterations 0.1382432 20.19737 at 10iterations 1.3425434E-02 2.747543 at 20iterations 1.3721131E-03 0.1941919 at 30iterations 1.5680092E-04 2.6605606E-02 at 40iterations 2.4465393E-05 3.4341812E-03 at 50iterations finished qdiffx linear iterations at : 17:02:41 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 2.4465393E-05 3.4341812E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 17:02:42 4.036u 0.259s 0:04.91 87.1% 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 17:02:42 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2283 !!! WARNING: GLM 55 has a net charge of -0.0940 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: 1.917483 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): -6.154000 39.56500 ymin,ymax (A): 15.97300 71.67101 zmin,zma (A): -0.7520000 48.13500 x,y,z range (A): 45.71900 55.69801 48.88700 scale (grids/A): 1.917483 object centre (A): 16.70550 43.82200 23.69150 number of atom coordinates read : 2283 total number of charged atoms : 2205 net assigned charge : -4.093994 assigned positive charge : 337.0143 centred at (gu) : 91.24895 89.01987 84.76823 assigned negative charge : -341.1089 centred at (gu) : 91.40121 89.02200 84.61913 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 68410 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20514 grid for indexing accessible points = 1.400000 m= 24321 mr = 46998 m= 4194 mr = 17599 m= 292 mr = 2608 m= 5 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 29910 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17376 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) : 0.6391611 object centre at (A) : 16.70550 43.82200 23.69150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7979380E-02 1.0280471E-02 midg,1,midg; midg,igrid,midg 1.6838433E-02 -7.7581117E-03 1,midg,midg; igrid,midg,midg -3.6605678E-03 -3.2373626E-02 gauss-seidel spectral radius is 0.9986274 estimated iterations to convergence 214 setup time was (sec) 0.9000000 now iterating at: 17:02:43 rms-change max change #iterations 4.003611 185.3560 at 10iterations 1.870678 66.10382 at 20iterations 0.8753293 33.01389 at 30iterations 0.4105258 15.82117 at 40iterations 0.1922050 6.406820 at 50iterations 8.9812540E-02 2.875508 at 60iterations 4.2243280E-02 1.313962 at 70iterations 1.9689819E-02 0.6516495 at 80iterations 9.2098434E-03 0.3028774 at 90iterations 4.3331413E-03 0.1561031 at 100iterations 2.0334786E-03 6.9834709E-02 at 110iterations 9.5677911E-04 3.5041809E-02 at 120iterations finished qdiffx linear iterations at : 17:02:51 total time elapsed so far: 9.090000 # loops : 120 mean,max change (kT/e) : 9.5677911E-04 3.5041809E-02 energy calculations done at 9.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.260000 DelPhi exited at 17:02:52 9.267u 0.304s 0:10.64 89.8% 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 Mon Oct 10 2011 at 17:02:53 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2283 !!! WARNING: GLM 55 has a net charge of -0.0940 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: 2.876225 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): -6.154000 39.56500 ymin,ymax (A): 15.97300 71.67101 zmin,zma (A): -0.7520000 48.13500 x,y,z range (A): 45.71900 55.69801 48.88700 scale (grids/A): 2.876225 object centre (A): 16.70550 43.82200 23.69150 number of atom coordinates read : 2283 total number of charged atoms : 2205 net assigned charge : -4.093994 assigned positive charge : 337.0143 centred at (gu) : 91.87327 88.52970 82.15220 assigned negative charge : -341.1089 centred at (gu) : 92.10175 88.53296 81.92860 start vw surface at 0.1400000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 158476 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20514 grid for indexing accessible points = 1.400000 m= 78454 mr = 114476 m= 28996 mr = 63340 m= 7433 mr = 22993 m= 1300 mr = 5573 m= 111 mr = 900 m= 4 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.580000 number of dielectric boundary points 67447 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 17635 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) : 1.917483 object centre at (A) : 16.70550 43.82200 23.69150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2961841 0.1615781 midg,1,midg; midg,igrid,midg 0.2007787 -3.5647150E-02 1,midg,midg; igrid,midg,midg -4.4416770E-02 -0.3110867 gauss-seidel spectral radius is 0.9992551 estimated iterations to convergence 289 setup time was (sec) 1.890000 now iterating at: 17:02:55 rms-change max change #iterations 9.420805 451.0724 at 10iterations 5.509631 142.7879 at 20iterations 3.215042 64.28132 at 30iterations 1.863747 40.78357 at 40iterations 1.081843 20.52689 at 50iterations 0.6253226 12.10796 at 60iterations 0.3611870 7.539749 at 70iterations 0.2080560 4.361917 at 80iterations 0.1197415 2.197729 at 90iterations 6.8936422E-02 1.304337 at 100iterations 3.9686337E-02 0.8544006 at 110iterations 2.2820223E-02 0.4230328 at 120iterations 1.3113307E-02 0.2284927 at 130iterations 7.5259162E-03 0.1458988 at 140iterations 4.3195751E-03 8.2607269E-02 at 150iterations 2.4831924E-03 4.5597076E-02 at 160iterations 1.4329096E-03 2.7726173E-02 at 170iterations 8.2955888E-04 1.5726089E-02 at 180iterations finished qdiffx linear iterations at : 17:03:08 total time elapsed so far: 15.30000 # loops : 180 mean,max change (kT/e) : 8.2955888E-04 1.5726089E-02 energy calculations done at 15.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.48000 DelPhi exited at 17:03:09 15.480u 0.320s 0:16.11 98.0% 0+0k 0+0io 0pf+0w