Mon Oct 10 22:52:45 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 Mon Oct 10 2011 at 22:52:45 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 = 2680 !!! WARNING: ASP 298 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: 0.6496113 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): -8.420000 46.38200 ymin,ymax (A): -15.29400 29.97000 zmin,zma (A): -11.48600 41.94600 x,y,z range (A): 54.80200 45.26400 53.43200 scale (grids/A): 0.6496113 object centre (A): 18.98100 7.338001 15.23000 number of atom coordinates read : 2680 total number of charged atoms : 2536 net assigned charge : 2.500015 assigned positive charge : 403.3306 centred at (gu) : 89.48478 90.09402 89.04845 assigned negative charge : -400.8313 centred at (gu) : 89.76773 90.04557 89.05987 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 7585 nv = 96 ne = 84 npr = 54606 no. pairs analyzed = 54606 no. exposed pairs = 3222 no. arc points = 22462 no. surface atoms = 1098 nbur = 1582 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 424 mr = 4312 m= 0 mr = 48 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 0.4300000 number of dielectric boundary points 3649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2115 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 8962 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7260216E-09 2.3110431E-09 midg,1,midg; midg,igrid,midg -2.9625506E-09 1.2315664E-08 1,midg,midg; igrid,midg,midg 5.2884850E-08 -3.6594791E-08 gauss-seidel spectral radius is 0.9877265 estimated iterations to convergence 74 setup time was (sec) 0.7200000 now iterating at: 22:52:46 rms-change max change #iterations 0.1551276 23.27584 at 10iterations 1.6883560E-02 2.266445 at 20iterations 2.3115557E-03 0.3885689 at 30iterations 5.5909960E-04 0.1162682 at 40iterations 1.7053781E-04 3.6113739E-02 at 50iterations finished qdiffx linear iterations at : 22:52:49 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 1.7053781E-04 3.6113739E-02 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 22:52:50 4.099u 0.136s 0:04.78 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 22:52:50 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 = 2680 !!! WARNING: ASP 298 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: 1.948834 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): -8.420000 46.38200 ymin,ymax (A): -15.29400 29.97000 zmin,zma (A): -11.48600 41.94600 x,y,z range (A): 54.80200 45.26400 53.43200 scale (grids/A): 1.948834 object centre (A): 18.98100 7.338001 15.23000 number of atom coordinates read : 2680 total number of charged atoms : 2536 net assigned charge : 2.500015 assigned positive charge : 403.3306 centred at (gu) : 88.45386 90.28143 87.14476 assigned negative charge : -400.8313 centred at (gu) : 89.30293 90.13644 87.17930 start vw surface at 0.1900000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 81789 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22462 grid for indexing accessible points = 1.400000 m= 30163 mr = 57406 m= 4879 mr = 22861 m= 270 mr = 3167 m= 2 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 969 time to turn everything in is 0.7500000 number of dielectric boundary points 33558 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 104 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 20026 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) : 0.6496113 object centre at (A) : 18.98100 7.338001 15.23000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7523687E-02 5.8121900E-03 midg,1,midg; midg,igrid,midg 1.8380139E-02 2.0263016E-02 1,midg,midg; igrid,midg,midg 5.4044198E-02 -6.6085882E-02 gauss-seidel spectral radius is 0.9986992 estimated iterations to convergence 220 setup time was (sec) 1.130000 now iterating at: 22:52:51 rms-change max change #iterations 4.519416 176.8095 at 10iterations 2.155692 74.31939 at 20iterations 1.028060 30.74948 at 30iterations 0.4880156 14.93684 at 40iterations 0.2332969 7.606867 at 50iterations 0.1118486 3.408758 at 60iterations 5.3352352E-02 1.678182 at 70iterations 2.5521742E-02 0.7269211 at 80iterations 1.2311662E-02 0.3596878 at 90iterations 6.0091894E-03 0.1774597 at 100iterations 2.9764923E-03 9.2548370E-02 at 110iterations 1.5371459E-03 5.3997040E-02 at 120iterations finished qdiffx linear iterations at : 22:53:00 total time elapsed so far: 9.590000 # loops : 120 mean,max change (kT/e) : 1.5371459E-03 5.3997040E-02 energy calculations done at 9.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.830000 DelPhi exited at 22:53:01 9.830u 0.268s 0:11.68 86.3% 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 Mon Oct 10 2011 at 22:53:02 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 = 2680 !!! WARNING: ASP 298 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.923251 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): -8.420000 46.38200 ymin,ymax (A): -15.29400 29.97000 zmin,zma (A): -11.48600 41.94600 x,y,z range (A): 54.80200 45.26400 53.43200 scale (grids/A): 2.923251 object centre (A): 18.98100 7.338001 15.23000 number of atom coordinates read : 2680 total number of charged atoms : 2536 net assigned charge : 2.500015 assigned positive charge : 403.3306 centred at (gu) : 87.68064 90.42179 85.71694 assigned negative charge : -400.8313 centred at (gu) : 88.95436 90.20454 85.76881 start vw surface at 0.2300000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 188836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22462 grid for indexing accessible points = 1.400000 m= 97295 mr = 138698 m= 36068 mr = 80739 m= 8892 mr = 29494 m= 1402 mr = 6923 m= 89 mr = 981 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 3344 time to turn everything in is 2.000000 number of dielectric boundary points 75695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 20288 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) : 1.948834 object centre at (A) : 18.98100 7.338001 15.23000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3294282 -4.3705933E-02 midg,1,midg; midg,igrid,midg 0.2744887 0.2081149 1,midg,midg; igrid,midg,midg 0.6543546 -0.6586020 gauss-seidel spectral radius is 0.9992705 estimated iterations to convergence 292 setup time was (sec) 2.400000 now iterating at: 22:53:05 rms-change max change #iterations 10.40952 423.3620 at 10iterations 6.068755 123.5641 at 20iterations 3.532214 73.91143 at 30iterations 2.043942 37.01672 at 40iterations 1.186129 24.30122 at 50iterations 0.6861787 13.14449 at 60iterations 0.3970286 7.285786 at 70iterations 0.2293714 3.950275 at 80iterations 0.1323890 2.436268 at 90iterations 7.6696880E-02 1.255534 at 100iterations 4.4209924E-02 0.7871284 at 110iterations 2.5651364E-02 0.4735699 at 120iterations 1.4847525E-02 0.2631664 at 130iterations 8.6602019E-03 0.1505318 at 140iterations 5.0860019E-03 8.7121964E-02 at 150iterations 3.0457943E-03 6.3312531E-02 at 160iterations 1.8641963E-03 4.2472839E-02 at 170iterations 1.1965863E-03 2.7935028E-02 at 180iterations finished qdiffx linear iterations at : 22:53:18 total time elapsed so far: 15.85000 # loops : 180 mean,max change (kT/e) : 1.1965863E-03 2.7935028E-02 energy calculations done at 15.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.08000 DelPhi exited at 22:53:19 16.083u 0.269s 0:16.84 97.0% 0+0k 0+0io 0pf+0w