Sat Oct 8 17:09:17 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 Sat Oct 8 2011 at 17:09:17 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 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: 0.5558158 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): 35.84000 93.26600 ymin,ymax (A): 16.45400 80.50400 zmin,zma (A): -21.61500 24.88700 x,y,z range (A): 57.42600 64.05000 46.50200 scale (grids/A): 0.5558158 object centre (A): 64.55300 48.47900 1.636000 number of atom coordinates read : 3366 total number of charged atoms : 3220 net assigned charge : -7.999982 assigned positive charge : 506.3726 centred at (gu) : 90.46715 90.09164 89.87041 assigned negative charge : -514.3738 centred at (gu) : 90.45394 90.04420 89.82542 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6775 nv = 96 ne = 84 npr = 67619 no. pairs analyzed = 67619 no. exposed pairs = 4248 no. arc points = 29084 no. surface atoms = 1434 nbur = 1932 mkacc time = 0.1900000 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 = 1.568000 m= 318 mr = 3639 m= 2 mr = 22 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 0.4000000 number of dielectric boundary points 3434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2967 ## 397 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8854 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2666111E-09 -2.2756978E-10 midg,1,midg; midg,igrid,midg -1.2276027E-09 -2.1112677E-10 1,midg,midg; igrid,midg,midg -7.8232903E-10 -6.4958677E-10 gauss-seidel spectral radius is 0.9833350 estimated iterations to convergence 64 setup time was (sec) 0.6700000 now iterating at: 17:09:18 rms-change max change #iterations 8.6123928E-02 15.17673 at 10iterations 6.1166757E-03 0.9904280 at 20iterations 4.6760187E-04 7.1166992E-02 at 30iterations 5.5161894E-05 1.0194778E-02 at 40iterations 1.1249827E-05 2.3984909E-03 at 50iterations finished qdiffx linear iterations at : 17:09:21 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 1.1249827E-05 2.3984909E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 17:09:22 4.120u 0.276s 0:04.71 93.2% 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 Sat Oct 8 2011 at 17:09:22 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 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: 1.667447 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): 35.84000 93.26600 ymin,ymax (A): 16.45400 80.50400 zmin,zma (A): -21.61500 24.88700 x,y,z range (A): 57.42600 64.05000 46.50200 scale (grids/A): 1.667447 object centre (A): 64.55300 48.47900 1.636000 number of atom coordinates read : 3366 total number of charged atoms : 3220 net assigned charge : -7.999982 assigned positive charge : 506.3726 centred at (gu) : 91.40082 90.27415 89.61036 assigned negative charge : -514.3738 centred at (gu) : 91.36150 90.13223 89.47604 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 75178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29084 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24929 mr = 52100 m= 2940 mr = 17525 m= 99 mr = 1506 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 496 time to turn everything in is 0.6800000 number of dielectric boundary points 32010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 311 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 24866 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) : 0.5558158 object centre at (A) : 64.55300 48.47900 1.636000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6945808E-03 -3.6703239E-03 midg,1,midg; midg,igrid,midg 5.3617316E-03 1.7645957E-02 1,midg,midg; igrid,midg,midg -2.4092967E-02 -7.7450159E-03 gauss-seidel spectral radius is 0.9983026 estimated iterations to convergence 193 setup time was (sec) 0.9900000 now iterating at: 17:09:23 rms-change max change #iterations 3.747757 177.1191 at 10iterations 1.608223 58.22681 at 20iterations 0.6892637 23.93286 at 30iterations 0.2957053 11.08155 at 40iterations 0.1272813 4.418514 at 50iterations 5.4719843E-02 1.995127 at 60iterations 2.3581533E-02 0.8063087 at 70iterations 1.0126633E-02 0.3345985 at 80iterations 4.3622670E-03 0.1497173 at 90iterations 1.8819233E-03 6.9129944E-02 at 100iterations 8.1772316E-04 2.7519703E-02 at 110iterations 3.5749335E-04 1.2223244E-02 at 120iterations finished qdiffx linear iterations at : 17:09:31 total time elapsed so far: 9.230000 # loops : 120 mean,max change (kT/e) : 3.5749335E-04 1.2223244E-02 energy calculations done at 9.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.400000 DelPhi exited at 17:09:32 9.401u 0.286s 0:10.07 96.1% 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 Sat Oct 8 2011 at 17:09:32 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 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: 2.501171 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): 35.84000 93.26600 ymin,ymax (A): 16.45400 80.50400 zmin,zma (A): -21.61500 24.88700 x,y,z range (A): 57.42600 64.05000 46.50200 scale (grids/A): 2.501171 object centre (A): 64.55300 48.47900 1.636000 number of atom coordinates read : 3366 total number of charged atoms : 3220 net assigned charge : -7.999982 assigned positive charge : 506.3726 centred at (gu) : 92.10106 90.41092 89.41526 assigned negative charge : -514.3738 centred at (gu) : 92.04209 90.19830 89.21381 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 174670 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29084 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 84521 mr = 127190 m= 25797 mr = 67568 m= 4752 mr = 19632 m= 414 mr = 3223 m= 12 mr = 212 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 1737 time to turn everything in is 1.670000 number of dielectric boundary points 72341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 25740 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) : 1.667447 object centre at (A) : 64.55300 48.47900 1.636000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1192129 -2.6668316E-02 midg,1,midg; midg,igrid,midg 0.2391597 0.4502133 1,midg,midg; igrid,midg,midg -0.3072370 -5.0674301E-02 gauss-seidel spectral radius is 0.9991793 estimated iterations to convergence 276 setup time was (sec) 2.000000 now iterating at: 17:09:34 rms-change max change #iterations 9.557925 342.7036 at 10iterations 5.426314 131.4932 at 20iterations 3.060071 61.99976 at 30iterations 1.721580 33.95433 at 40iterations 0.9695529 19.45381 at 50iterations 0.5432070 10.17065 at 60iterations 0.3036731 6.344319 at 70iterations 0.1700031 3.687283 at 80iterations 9.5030770E-02 1.889413 at 90iterations 5.3114556E-02 0.9593425 at 100iterations 2.9640881E-02 0.5765972 at 110iterations 1.6581787E-02 0.3217087 at 120iterations 9.2571359E-03 0.1716805 at 130iterations 5.1739351E-03 0.1035137 at 140iterations 2.9021499E-03 5.4284692E-02 at 150iterations 1.6316158E-03 3.2915115E-02 at 160iterations 9.1949792E-04 1.6525269E-02 at 170iterations 5.2634237E-04 1.0391235E-02 at 180iterations finished qdiffx linear iterations at : 17:09:48 total time elapsed so far: 15.58000 # loops : 180 mean,max change (kT/e) : 5.2634237E-04 1.0391235E-02 energy calculations done at 15.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.77000 DelPhi exited at 17:09:48 15.772u 0.283s 0:16.31 98.4% 0+0k 0+0io 0pf+0w