Wed Feb 15 08:54:59 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_thinner.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 Wed Feb 15 2012 at 08:54:59 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= 9.0000004E-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 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6303 nv = 96 ne = 84 npr = 48327 no. pairs analyzed = 48327 no. exposed pairs = 2756 no. arc points = 19642 no. surface atoms = 928 nbur = 1299 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 3361 m= 0 mr = 43 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2900000 number of dielectric boundary points 3269 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1774 ## 121 charges are in solution ## iepsmp to db, and charging done at 0.3900000 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 0.9879129 estimated iterations to convergence 74 setup time was (sec) 0.5100000 now iterating at: 08:55:00 rms-change max change #iterations 0.1480248 22.34519 at 10iterations 1.5343551E-02 2.480164 at 20iterations 1.5927404E-03 0.2164068 at 30iterations 1.6595889E-04 2.5142670E-02 at 40iterations 1.7272321E-05 2.8533936E-03 at 50iterations finished qdiffx linear iterations at : 08:55:02 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 1.7272321E-05 2.8533936E-03 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 08:55:03 3.181u 0.158s 0:03.82 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 Wed Feb 15 2012 at 08:55:03 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 # 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: 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 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 67097 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19642 grid for indexing accessible points = 1.400000 m= 23962 mr = 45367 m= 4179 mr = 17436 m= 313 mr = 2644 m= 7 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 29963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.6100000 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 -2.4511073E-02 -9.8074064E-02 midg,1,midg; midg,igrid,midg 6.2092748E-03 8.4073124E-03 1,midg,midg; igrid,midg,midg -6.7897186E-02 4.9842061E-03 gauss-seidel spectral radius is 0.9986811 estimated iterations to convergence 218 setup time was (sec) 0.7500000 now iterating at: 08:55:04 rms-change max change #iterations 4.092782 203.7516 at 10iterations 1.929144 73.24309 at 20iterations 0.9129766 29.38388 at 30iterations 0.4356039 16.34632 at 40iterations 0.2059355 7.169559 at 50iterations 9.7365566E-02 3.234907 at 60iterations 4.6171021E-02 1.605762 at 70iterations 2.1921927E-02 0.7354355 at 80iterations 1.0365541E-02 0.3416150 at 90iterations 4.9307817E-03 0.1643829 at 100iterations 2.3311127E-03 7.4900627E-02 at 110iterations 1.1053322E-03 3.6520243E-02 at 120iterations finished qdiffx linear iterations at : 08:55:10 total time elapsed so far: 7.130000 # loops : 120 mean,max change (kT/e) : 1.1053322E-03 3.6520243E-02 energy calculations done at 7.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.310000 DelPhi exited at 08:55:11 7.308u 0.192s 0:07.89 94.9% 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 Wed Feb 15 2012 at 08:55:11 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= 0.1000000 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 0.1900000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 155620 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19642 grid for indexing accessible points = 1.400000 m= 76077 mr = 110532 m= 28878 mr = 61578 m= 7704 mr = 23034 m= 1433 mr = 5835 m= 112 mr = 1077 m= 0 mr = 53 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.340000 number of dielectric boundary points 67715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.470000 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 -0.1273237 -1.525956 midg,1,midg; midg,igrid,midg 8.0142409E-02 4.7347225E-02 1,midg,midg; igrid,midg,midg -0.7138141 -0.1716941 gauss-seidel spectral radius is 0.9992704 estimated iterations to convergence 292 setup time was (sec) 1.620000 now iterating at: 08:55:13 rms-change max change #iterations 9.359328 398.8365 at 10iterations 5.404065 141.8930 at 20iterations 3.120914 61.86740 at 30iterations 1.801880 35.40889 at 40iterations 1.036867 22.14543 at 50iterations 0.5974547 10.92671 at 60iterations 0.3443794 6.621397 at 70iterations 0.1989531 3.868130 at 80iterations 0.1141030 2.159912 at 90iterations 6.5751784E-02 1.234586 at 100iterations 3.7843116E-02 0.7168121 at 110iterations 2.1747718E-02 0.4102936 at 120iterations 1.2528476E-02 0.2366257 at 130iterations 7.2237868E-03 0.1325150 at 140iterations 4.1578370E-03 8.8272095E-02 at 150iterations 2.3919081E-03 4.2791367E-02 at 160iterations 1.3754573E-03 2.5252342E-02 at 170iterations 7.9195178E-04 1.3732910E-02 at 180iterations finished qdiffx linear iterations at : 08:55:22 total time elapsed so far: 11.08000 # loops : 180 mean,max change (kT/e) : 7.9195178E-04 1.3732910E-02 energy calculations done at 11.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.27000 DelPhi exited at 08:55:23 11.274u 0.201s 0:12.02 95.4% 0+0k 0+0io 0pf+0w