Tue Oct 11 07:57:19 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 Tue Oct 11 2011 at 07:57:19 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6573603 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): -2.427000 51.72900 ymin,ymax (A): -22.13200 22.81500 zmin,zma (A): 8.816000 53.82200 x,y,z range (A): 54.15600 44.94700 45.00600 scale (grids/A): 0.6573603 object centre (A): 24.65100 0.3415003 31.31900 number of atom coordinates read : 2358 total number of charged atoms : 2216 net assigned charge : 4.945009 assigned positive charge : 354.8774 centred at (gu) : 89.41698 90.24452 90.16742 assigned negative charge : -349.9328 centred at (gu) : 89.44923 90.19999 89.97459 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6845 nv = 96 ne = 84 npr = 47999 no. pairs analyzed = 47999 no. exposed pairs = 2785 no. arc points = 19517 no. surface atoms = 937 nbur = 1421 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 373 mr = 3919 m= 5 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2700000 number of dielectric boundary points 3262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1916 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8044 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0434598E-08 4.4666297E-08 midg,1,midg; midg,igrid,midg 3.9824504E-09 1.9995518E-08 1,midg,midg; igrid,midg,midg 1.9146299E-08 5.5712550E-09 gauss-seidel spectral radius is 0.9879817 estimated iterations to convergence 74 setup time was (sec) 0.4800000 now iterating at: 07:57:19 rms-change max change #iterations 0.1551538 26.64425 at 10iterations 1.6652755E-02 2.314903 at 20iterations 1.7719467E-03 0.2682819 at 30iterations 1.8776202E-04 2.7694702E-02 at 40iterations 1.9372397E-05 2.9296875E-03 at 50iterations finished qdiffx linear iterations at : 07:57:22 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 1.9372397E-05 2.9296875E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 07:57:22 3.110u 0.161s 0:03.58 91.3% 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 07:57:22 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.972081 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): -2.427000 51.72900 ymin,ymax (A): -22.13200 22.81500 zmin,zma (A): 8.816000 53.82200 x,y,z range (A): 54.15600 44.94700 45.00600 scale (grids/A): 1.972081 object centre (A): 24.65100 0.3415003 31.31900 number of atom coordinates read : 2358 total number of charged atoms : 2216 net assigned charge : 4.945009 assigned positive charge : 354.8774 centred at (gu) : 88.25060 90.73322 90.50204 assigned negative charge : -349.9328 centred at (gu) : 88.34761 90.59980 89.92361 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19517 grid for indexing accessible points = 1.400000 m= 26990 mr = 51599 m= 4122 mr = 20229 m= 297 mr = 2550 m= 8 mr = 130 m= 0 mr = 2 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2105 time to turn everything in is 0.5100000 number of dielectric boundary points 30150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 139 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 17463 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) : 0.6573603 object centre at (A) : 24.65100 0.3415003 31.31900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5086273E-02 4.8143946E-02 midg,1,midg; midg,igrid,midg -1.2585580E-03 5.3089247E-03 1,midg,midg; igrid,midg,midg 2.5289802E-02 3.1146090E-02 gauss-seidel spectral radius is 0.9986967 estimated iterations to convergence 219 setup time was (sec) 0.7800000 now iterating at: 07:57:23 rms-change max change #iterations 4.270090 178.7047 at 10iterations 2.036710 69.78487 at 20iterations 0.9744562 32.39487 at 30iterations 0.4651181 16.26163 at 40iterations 0.2227971 7.290764 at 50iterations 0.1064595 3.335907 at 60iterations 5.0827082E-02 1.822906 at 70iterations 2.4207542E-02 0.7475030 at 80iterations 1.1580335E-02 0.3659109 at 90iterations 5.5045080E-03 0.1692467 at 100iterations 2.6270694E-03 8.6399078E-02 at 110iterations 1.2554891E-03 4.1846275E-02 at 120iterations finished qdiffx linear iterations at : 07:57:29 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 1.2554891E-03 4.1846275E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 07:57:30 6.967u 0.190s 0:07.48 95.5% 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 07:57:30 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.958121 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): -2.427000 51.72900 ymin,ymax (A): -22.13200 22.81500 zmin,zma (A): 8.816000 53.82200 x,y,z range (A): 54.15600 44.94700 45.00600 scale (grids/A): 2.958121 object centre (A): 24.65100 0.3415003 31.31900 number of atom coordinates read : 2358 total number of charged atoms : 2216 net assigned charge : 4.945009 assigned positive charge : 354.8774 centred at (gu) : 87.37582 91.09979 90.75295 assigned negative charge : -349.9328 centred at (gu) : 87.52145 90.89975 89.88544 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 169279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19517 grid for indexing accessible points = 1.400000 m= 87302 mr = 124660 m= 31571 mr = 72359 m= 7167 mr = 25605 m= 1160 mr = 5267 m= 98 mr = 834 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 7018 time to turn everything in is 1.280000 number of dielectric boundary points 67811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 17724 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) : 1.972081 object centre at (A) : 24.65100 0.3415003 31.31900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3224947 0.4875633 midg,1,midg; midg,igrid,midg -3.9903443E-02 -2.3704672E-02 1,midg,midg; igrid,midg,midg 5.8309998E-02 9.1592178E-02 gauss-seidel spectral radius is 0.9992629 estimated iterations to convergence 291 setup time was (sec) 1.560000 now iterating at: 07:57:32 rms-change max change #iterations 9.726945 444.1448 at 10iterations 5.636113 117.6077 at 20iterations 3.259766 66.50951 at 30iterations 1.882343 38.08815 at 40iterations 1.087977 19.01469 at 50iterations 0.6258369 11.98425 at 60iterations 0.3613199 6.460403 at 70iterations 0.2078929 3.695727 at 80iterations 0.1196191 2.116417 at 90iterations 6.8989642E-02 1.230753 at 100iterations 3.9607875E-02 0.7174919 at 110iterations 2.2805713E-02 0.4937596 at 120iterations 1.3133967E-02 0.2341795 at 130iterations 7.5664460E-03 0.1370564 at 140iterations 4.3734140E-03 8.1748962E-02 at 150iterations 2.5212141E-03 4.7385216E-02 at 160iterations 1.4601445E-03 2.4479389E-02 at 170iterations 8.5075683E-04 1.4633179E-02 at 180iterations finished qdiffx linear iterations at : 07:57:42 total time elapsed so far: 11.64000 # loops : 180 mean,max change (kT/e) : 8.5075683E-04 1.4633179E-02 energy calculations done at 11.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.83000 DelPhi exited at 07:57:42 11.828u 0.203s 0:12.40 96.9% 0+0k 0+0io 0pf+0w