Tue Oct 11 03:36:11 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 03:36:11 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 = 2227 !!! WARNING: ASP 461 has a net charge of -2.0000 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: 0.6556773 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): -12.62900 38.70800 ymin,ymax (A): 2.377000 40.96100 zmin,zma (A): 27.80400 82.09900 x,y,z range (A): 51.33700 38.58400 54.29500 scale (grids/A): 0.6556773 object centre (A): 13.03950 21.66900 54.95150 number of atom coordinates read : 2227 total number of charged atoms : 2087 net assigned charge : -4.499989 assigned positive charge : 321.2875 centred at (gu) : 90.71135 90.79617 90.47636 assigned negative charge : -325.7878 centred at (gu) : 90.40166 90.77695 90.63960 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6339 nv = 96 ne = 84 npr = 47345 no. pairs analyzed = 47345 no. exposed pairs = 2766 no. arc points = 19608 no. surface atoms = 932 nbur = 1295 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 373 mr = 3414 m= 0 mr = 42 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1762 ## 120 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7456 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2145367E-08 -3.8682991E-08 midg,1,midg; midg,igrid,midg -1.1207087E-08 -8.7536858E-09 1,midg,midg; igrid,midg,midg -4.9792046E-08 3.9892551E-08 gauss-seidel spectral radius is 0.9879132 estimated iterations to convergence 74 setup time was (sec) 0.5600000 now iterating at: 03:36:12 rms-change max change #iterations 0.1485516 22.36659 at 10iterations 1.5286343E-02 2.258156 at 20iterations 1.5959064E-03 0.2172012 at 30iterations 1.6648683E-04 2.2785187E-02 at 40iterations 1.7236134E-05 2.5291443E-03 at 50iterations finished qdiffx linear iterations at : 03:36:14 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.7236134E-05 2.5291443E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 03:36:15 3.559u 0.197s 0:04.21 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 03:36:15 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2227 !!! WARNING: ASP 461 has a net charge of -2.0000 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: 1.967032 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): -12.62900 38.70800 ymin,ymax (A): 2.377000 40.96100 zmin,zma (A): 27.80400 82.09900 x,y,z range (A): 51.33700 38.58400 54.29500 scale (grids/A): 1.967032 object centre (A): 13.03950 21.66900 54.95150 number of atom coordinates read : 2227 total number of charged atoms : 2087 net assigned charge : -4.499989 assigned positive charge : 321.2875 centred at (gu) : 92.13385 92.38802 91.42886 assigned negative charge : -325.7878 centred at (gu) : 91.20509 92.33088 91.91888 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 67627 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19608 grid for indexing accessible points = 1.400000 m= 24126 mr = 45944 m= 4143 mr = 17636 m= 293 mr = 2616 m= 7 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 372 time to turn everything in is 0.5900000 number of dielectric boundary points 29862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 16504 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) : 0.6556773 object centre at (A) : 13.03950 21.66900 54.95150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5226444E-02 -9.8060884E-02 midg,1,midg; midg,igrid,midg 6.2197712E-03 8.8368058E-03 1,midg,midg; igrid,midg,midg -6.7831486E-02 5.0170971E-03 gauss-seidel spectral radius is 0.9986810 estimated iterations to convergence 218 setup time was (sec) 0.9000000 now iterating at: 03:36:16 rms-change max change #iterations 4.092144 203.7484 at 10iterations 1.929967 73.24064 at 20iterations 0.9133179 29.55952 at 30iterations 0.4359246 16.34248 at 40iterations 0.2060779 6.648848 at 50iterations 9.7495556E-02 3.270458 at 60iterations 4.6218984E-02 1.640105 at 70iterations 2.1925226E-02 0.6884499 at 80iterations 1.0395921E-02 0.3247509 at 90iterations 4.9406416E-03 0.1606789 at 100iterations 2.3348809E-03 7.7564240E-02 at 110iterations 1.1083301E-03 3.5848379E-02 at 120iterations finished qdiffx linear iterations at : 03:36:23 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 1.1083301E-03 3.5848379E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 03:36:24 8.022u 0.225s 0:08.58 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 Tue Oct 11 2011 at 03:36:24 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 = 2227 !!! WARNING: ASP 461 has a net charge of -2.0000 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: 2.950548 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): -12.62900 38.70800 ymin,ymax (A): 2.377000 40.96100 zmin,zma (A): 27.80400 82.09900 x,y,z range (A): 51.33700 38.58400 54.29500 scale (grids/A): 2.950548 object centre (A): 13.03950 21.66900 54.95150 number of atom coordinates read : 2227 total number of charged atoms : 2087 net assigned charge : -4.499989 assigned positive charge : 321.2875 centred at (gu) : 93.20071 93.58206 92.14321 assigned negative charge : -325.7878 centred at (gu) : 91.80756 93.49619 92.87820 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 156777 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19608 grid for indexing accessible points = 1.400000 m= 76818 mr = 111775 m= 28986 mr = 62406 m= 7608 mr = 23187 m= 1351 mr = 5747 m= 98 mr = 1012 m= 0 mr = 44 time to grow re-entrant surface = 0.7600001 no. cavity mid-points inaccessible to solvent = 1297 time to turn everything in is 1.350000 number of dielectric boundary points 67467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 16696 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) : 1.967032 object centre at (A) : 13.03950 21.66900 54.95150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1303005 -1.525920 midg,1,midg; midg,igrid,midg 8.0365762E-02 5.1437378E-02 1,midg,midg; igrid,midg,midg -0.7133354 -0.1718263 gauss-seidel spectral radius is 0.9992704 estimated iterations to convergence 292 setup time was (sec) 1.670000 now iterating at: 03:36:26 rms-change max change #iterations 9.359421 398.8453 at 10iterations 5.405079 141.8993 at 20iterations 3.121289 61.57378 at 30iterations 1.802274 35.41201 at 40iterations 1.037512 21.80119 at 50iterations 0.5979612 11.07211 at 60iterations 0.3445036 6.397170 at 70iterations 0.1991078 3.659265 at 80iterations 0.1142533 2.041290 at 90iterations 6.5794289E-02 1.277824 at 100iterations 3.7849236E-02 0.7013130 at 110iterations 2.1784624E-02 0.4085307 at 120iterations 1.2548949E-02 0.2404785 at 130iterations 7.2327275E-03 0.1340008 at 140iterations 4.1639088E-03 8.7638855E-02 at 150iterations 2.3955798E-03 4.4658661E-02 at 160iterations 1.3772277E-03 2.7119637E-02 at 170iterations 7.9335459E-04 1.4083862E-02 at 180iterations finished qdiffx linear iterations at : 03:36:37 total time elapsed so far: 12.57000 # loops : 180 mean,max change (kT/e) : 7.9335459E-04 1.4083862E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 03:36:37 12.759u 0.286s 0:13.80 94.4% 0+0k 0+0io 0pf+0w