Mon Oct 10 14:11:30 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 14:11:30 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: 348 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3208 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5625523 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): 23.88700 81.16900 ymin,ymax (A): 20.18800 83.47100 zmin,zma (A): 3.979000 58.68100 x,y,z range (A): 57.28200 63.28300 54.70200 scale (grids/A): 0.5625523 object centre (A): 52.52800 51.82950 31.33000 number of atom coordinates read : 3208 total number of charged atoms : 3027 net assigned charge : -1.499995 assigned positive charge : 483.3977 centred at (gu) : 88.94771 89.79331 88.01544 assigned negative charge : -484.8989 centred at (gu) : 89.00160 89.90509 88.03759 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6533 nv = 96 ne = 84 npr = 65930 no. pairs analyzed = 65930 no. exposed pairs = 4169 no. arc points = 28476 no. surface atoms = 1408 nbur = 1800 mkacc time = 0.1100000 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= 290 mr = 3389 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2908 ## 333 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8481 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6861178E-10 -3.0161615E-10 midg,1,midg; midg,igrid,midg 1.3246501E-09 -1.5996263E-09 1,midg,midg; igrid,midg,midg 6.6736378E-10 -7.0222106E-10 gauss-seidel spectral radius is 0.9837163 estimated iterations to convergence 64 setup time was (sec) 0.4300000 now iterating at: 14:11:30 rms-change max change #iterations 8.9557186E-02 17.69208 at 10iterations 6.7710136E-03 1.171312 at 20iterations 7.1276276E-04 0.1221008 at 30iterations 1.3151512E-04 2.1946430E-02 at 40iterations 3.0259533E-05 5.1193237E-03 at 50iterations finished qdiffx linear iterations at : 14:11:33 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.0259533E-05 5.1193237E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 14:11:33 3.385u 0.159s 0:03.93 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 14:11:34 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: 348 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3208 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.687657 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): 23.88700 81.16900 ymin,ymax (A): 20.18800 83.47100 zmin,zma (A): 3.979000 58.68100 x,y,z range (A): 57.28200 63.28300 54.70200 scale (grids/A): 1.687657 object centre (A): 52.52800 51.82950 31.33000 number of atom coordinates read : 3208 total number of charged atoms : 3027 net assigned charge : -1.499995 assigned positive charge : 483.3977 centred at (gu) : 86.84214 89.37909 84.04518 assigned negative charge : -484.8989 centred at (gu) : 87.00466 89.71517 84.11256 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72433 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28476 grid for indexing accessible points = 1.400000 m= 22636 mr = 49366 m= 2721 mr = 15336 m= 111 mr = 1379 m= 0 mr = 8 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 31812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 270 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 23430 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) : 0.5625523 object centre at (A) : 52.52800 51.82950 31.33000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0008601E-02 -1.4565687E-02 midg,1,midg; midg,igrid,midg 2.4763895E-02 -2.1976472E-03 1,midg,midg; igrid,midg,midg 5.7905996E-03 1.1040298E-03 gauss-seidel spectral radius is 0.9983270 estimated iterations to convergence 194 setup time was (sec) 0.5600000 now iterating at: 14:11:34 rms-change max change #iterations 3.736970 188.7830 at 10iterations 1.605200 63.75965 at 20iterations 0.6923421 24.93038 at 30iterations 0.2991967 10.96999 at 40iterations 0.1293337 4.372480 at 50iterations 5.5792041E-02 1.816082 at 60iterations 2.4078794E-02 0.8334160 at 70iterations 1.0482113E-02 0.3238850 at 80iterations 4.5909910E-03 0.1536674 at 90iterations 2.0251740E-03 6.8500519E-02 at 100iterations 9.0637879E-04 2.7719498E-02 at 110iterations 4.2004834E-04 1.3996124E-02 at 120iterations finished qdiffx linear iterations at : 14:11:41 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 4.2004834E-04 1.3996124E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 14:11:42 7.607u 0.206s 0:08.84 88.2% 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 14:11:42 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: 348 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3208 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.531486 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): 23.88700 81.16900 ymin,ymax (A): 20.18800 83.47100 zmin,zma (A): 3.979000 58.68100 x,y,z range (A): 57.28200 63.28300 54.70200 scale (grids/A): 2.531486 object centre (A): 52.52800 51.82950 31.33000 number of atom coordinates read : 3208 total number of charged atoms : 3027 net assigned charge : -1.499995 assigned positive charge : 483.3977 centred at (gu) : 85.26290 89.06843 81.06765 assigned negative charge : -484.8989 centred at (gu) : 85.50690 89.57261 81.16885 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 168494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28476 grid for indexing accessible points = 1.400000 m= 77784 mr = 121175 m= 23015 mr = 60982 m= 4424 mr = 16942 m= 427 mr = 3012 m= 4 mr = 188 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 71849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 24202 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) : 1.687657 object centre at (A) : 52.52800 51.82950 31.33000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1510964 -0.2553103 midg,1,midg; midg,igrid,midg 0.6885153 -5.5451058E-02 1,midg,midg; igrid,midg,midg 0.1610145 1.4648782E-04 gauss-seidel spectral radius is 0.9991856 estimated iterations to convergence 277 setup time was (sec) 1.100000 now iterating at: 14:11:44 rms-change max change #iterations 9.662727 358.6028 at 10iterations 5.548080 126.2696 at 20iterations 3.149546 72.45427 at 30iterations 1.787926 39.70823 at 40iterations 1.009676 21.69878 at 50iterations 0.5687430 11.73677 at 60iterations 0.3203397 6.370034 at 70iterations 0.1796788 3.443368 at 80iterations 0.1008319 2.027115 at 90iterations 5.6519289E-02 1.116508 at 100iterations 3.1641498E-02 0.6401672 at 110iterations 1.7764602E-02 0.3499527 at 120iterations 9.9428715E-03 0.2063966 at 130iterations 5.5820593E-03 0.1064682 at 140iterations 3.1482410E-03 6.2841415E-02 at 150iterations 1.7807392E-03 3.8560867E-02 at 160iterations 1.0152052E-03 1.9273758E-02 at 170iterations 5.8964698E-04 1.1524200E-02 at 180iterations finished qdiffx linear iterations at : 14:11:55 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 5.8964698E-04 1.1524200E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 14:11:55 12.314u 0.226s 0:13.01 96.3% 0+0k 0+0io 0pf+0w