Sun Oct 9 22:10:40 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 Sun Oct 9 2011 at 22:10:40 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 = 3187 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: 0.5656540 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): -18.06800 37.91000 ymin,ymax (A): -4.408000 58.52800 zmin,zma (A): -5.052000 47.21500 x,y,z range (A): 55.97800 62.93600 52.26700 scale (grids/A): 0.5656540 object centre (A): 9.921000 27.06000 21.08150 number of atom coordinates read : 3187 total number of charged atoms : 3061 net assigned charge : 4.500014 assigned positive charge : 486.6807 centred at (gu) : 91.30222 88.67484 89.44131 assigned negative charge : -482.1821 centred at (gu) : 91.34769 88.58354 89.44234 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6671 nv = 96 ne = 84 npr = 61743 no. pairs analyzed = 61743 no. exposed pairs = 4243 no. arc points = 30745 no. surface atoms = 1418 nbur = 1769 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 289 mr = 3327 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3015 ## 382 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8620 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2057393E-10 5.2921162E-10 midg,1,midg; midg,igrid,midg -1.0247484E-09 1.4112795E-09 1,midg,midg; igrid,midg,midg 9.3872154E-10 -8.1564082E-11 gauss-seidel spectral radius is 0.9838985 estimated iterations to convergence 65 setup time was (sec) 0.4200000 now iterating at: 22:10:41 rms-change max change #iterations 8.9524180E-02 13.58454 at 10iterations 6.4274576E-03 1.122902 at 20iterations 4.7606992E-04 7.4754715E-02 at 30iterations 3.5216177E-05 5.2394867E-03 at 40iterations 2.5809868E-06 4.2343140E-04 at 50iterations finished qdiffx linear iterations at : 22:10:44 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 2.5809868E-06 4.2343140E-04 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 22:10:44 3.487u 0.173s 0:03.93 92.8% 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 Sun Oct 9 2011 at 22:10:44 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 = 3187 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: 1.696962 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): -18.06800 37.91000 ymin,ymax (A): -4.408000 58.52800 zmin,zma (A): -5.052000 47.21500 x,y,z range (A): 55.97800 62.93600 52.26700 scale (grids/A): 1.696962 object centre (A): 9.921000 27.06000 21.08150 number of atom coordinates read : 3187 total number of charged atoms : 3061 net assigned charge : 4.500014 assigned positive charge : 486.6807 centred at (gu) : 93.90562 86.02370 88.32281 assigned negative charge : -482.1821 centred at (gu) : 94.04295 85.75056 88.32681 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73152 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30745 grid for indexing accessible points = 1.400000 m= 22246 mr = 48211 m= 2526 mr = 14860 m= 114 mr = 1233 m= 6 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 177 time to turn everything in is 0.3600000 number of dielectric boundary points 33717 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 321 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 23594 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) : 0.5656540 object centre at (A) : 9.921000 27.06000 21.08150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0309873E-03 -6.3318585E-06 midg,1,midg; midg,igrid,midg -7.0422632E-03 -8.1961583E-03 1,midg,midg; igrid,midg,midg -1.3522673E-03 1.1895921E-02 gauss-seidel spectral radius is 0.9983574 estimated iterations to convergence 196 setup time was (sec) 0.5800000 now iterating at: 22:10:45 rms-change max change #iterations 3.756815 191.3156 at 10iterations 1.636278 66.32796 at 20iterations 0.7085814 24.38148 at 30iterations 0.3058183 12.39707 at 40iterations 0.1333696 4.528694 at 50iterations 5.8025114E-02 2.016917 at 60iterations 2.5150564E-02 0.8433228 at 70iterations 1.0924032E-02 0.4149914 at 80iterations 4.7681620E-03 0.1595345 at 90iterations 2.0700188E-03 7.2271347E-02 at 100iterations 8.9848292E-04 3.1787872E-02 at 110iterations 3.9210246E-04 1.2847900E-02 at 120iterations finished qdiffx linear iterations at : 22:10:52 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 3.9210246E-04 1.2847900E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 22:10:53 7.952u 0.203s 0:08.73 93.3% 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 Sun Oct 9 2011 at 22:10:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3187 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: 2.545443 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): -18.06800 37.91000 ymin,ymax (A): -4.408000 58.52800 zmin,zma (A): -5.052000 47.21500 x,y,z range (A): 55.97800 62.93600 52.26700 scale (grids/A): 2.545443 object centre (A): 9.921000 27.06000 21.08150 number of atom coordinates read : 3187 total number of charged atoms : 3061 net assigned charge : 4.500014 assigned positive charge : 486.6807 centred at (gu) : 95.85828 84.03542 87.48403 assigned negative charge : -482.1821 centred at (gu) : 96.06446 83.62569 87.49014 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 170013 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30745 grid for indexing accessible points = 1.400000 m= 76319 mr = 118478 m= 22235 mr = 59127 m= 4000 mr = 16395 m= 411 mr = 2588 m= 24 mr = 219 m= 0 mr = 4 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 574 time to turn everything in is 0.8900000 number of dielectric boundary points 76191 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 24466 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) : 1.696962 object centre at (A) : 9.921000 27.06000 21.08150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3075866E-02 2.9137656E-03 midg,1,midg; midg,igrid,midg -0.2355785 -0.4792792 1,midg,midg; igrid,midg,midg -0.1165938 0.1853014 gauss-seidel spectral radius is 0.9992014 estimated iterations to convergence 279 setup time was (sec) 1.120000 now iterating at: 22:10:54 rms-change max change #iterations 9.644979 314.8476 at 10iterations 5.609879 195.4945 at 20iterations 3.227251 78.92815 at 30iterations 1.847138 47.32207 at 40iterations 1.057857 26.99839 at 50iterations 0.6015599 14.47703 at 60iterations 0.3409218 8.080643 at 70iterations 0.1934554 3.980103 at 80iterations 0.1093243 2.256654 at 90iterations 6.1823167E-02 1.358023 at 100iterations 3.4844786E-02 0.7121391 at 110iterations 1.9661814E-02 0.4004078 at 120iterations 1.1103703E-02 0.2152252 at 130iterations 6.2472466E-03 0.1264524 at 140iterations 3.5234503E-03 6.9657326E-02 at 150iterations 1.9831315E-03 3.9600372E-02 at 160iterations 1.1164395E-03 2.3417950E-02 at 170iterations 6.2842201E-04 1.1944771E-02 at 180iterations finished qdiffx linear iterations at : 22:11:06 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 6.2842201E-04 1.1944771E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 22:11:06 12.717u 0.224s 0:13.37 96.7% 0+0k 0+0io 0pf+0w