Sun Oct 9 15:40:27 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 15:40:27 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 = 5672 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5016699 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): 67.35700 138.3200 ymin,ymax (A): -6.168000 57.04100 zmin,zma (A): -3.345000 66.68100 x,y,z range (A): 70.96299 63.20900 70.02600 scale (grids/A): 0.5016699 object centre (A): 102.8385 25.43650 31.66800 number of atom coordinates read : 5672 total number of charged atoms : 5501 net assigned charge : -2.499966 assigned positive charge : 866.7610 centred at (gu) : 89.80852 90.84179 89.94879 assigned negative charge : -869.2690 centred at (gu) : 89.86953 90.77790 90.05084 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8621 nv = 96 ne = 84 npr = 117871 no. pairs analyzed = 117871 no. exposed pairs = 6440 no. arc points = 44899 no. surface atoms = 2162 nbur = 3510 mkacc time = 0.2500000 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 = 1.708000 m= 302 mr = 4668 m= 0 mr = 8 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.5100000 number of dielectric boundary points 4247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4315 ## 622 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 11881 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9300792E-10 -2.4340896E-10 midg,1,midg; midg,igrid,midg -1.3013891E-10 1.3928625E-10 1,midg,midg; igrid,midg,midg 1.1001280E-10 -1.4904571E-10 gauss-seidel spectral radius is 0.9797323 estimated iterations to convergence 58 setup time was (sec) 0.7200000 now iterating at: 15:40:28 rms-change max change #iterations 6.7874812E-02 9.953093 at 10iterations 4.5057843E-03 0.5966339 at 20iterations 8.3446020E-04 0.1317978 at 30iterations 2.5223361E-04 4.0028572E-02 at 40iterations 7.9067067E-05 1.2269974E-02 at 50iterations finished qdiffx linear iterations at : 15:40:30 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 7.9067067E-05 1.2269974E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 15:40:31 3.335u 0.139s 0:03.76 92.0% 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 15:40:31 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 = 5672 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1900000 grid size : 179 scale,in grids/A, set to be: 1.505010 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): 67.35700 138.3200 ymin,ymax (A): -6.168000 57.04100 zmin,zma (A): -3.345000 66.68100 x,y,z range (A): 70.96299 63.20900 70.02600 scale (grids/A): 1.505010 object centre (A): 102.8385 25.43650 31.66800 number of atom coordinates read : 5672 total number of charged atoms : 5501 net assigned charge : -2.499966 assigned positive charge : 866.7610 centred at (gu) : 89.42394 92.52341 89.84448 assigned negative charge : -869.2690 centred at (gu) : 89.60879 92.33361 90.15240 start vw surface at 0.2600000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 99575 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44899 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 28502 mr = 70456 m= 2394 mr = 19392 m= 47 mr = 1026 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 3924 time to turn everything in is 0.7200000 number of dielectric boundary points 39644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 604 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 41041 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) : 0.5016699 object centre at (A) : 102.8385 25.43650 31.66800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3480781E-03 3.0921793E-03 midg,1,midg; midg,igrid,midg -9.2099197E-03 6.0857194E-03 1,midg,midg; igrid,midg,midg -1.7308576E-02 -8.2265744E-03 gauss-seidel spectral radius is 0.9981027 estimated iterations to convergence 182 setup time was (sec) 1.000000 now iterating at: 15:40:32 rms-change max change #iterations 4.060426 158.6656 at 10iterations 1.658916 54.06378 at 20iterations 0.6790656 22.00253 at 30iterations 0.2789909 8.919070 at 40iterations 0.1140953 3.811056 at 50iterations 4.6947982E-02 1.424463 at 60iterations 1.9337138E-02 0.5595684 at 70iterations 7.9853134E-03 0.2510543 at 80iterations 3.3513401E-03 0.1004372 at 90iterations 1.4398575E-03 5.3276062E-02 at 100iterations 6.5140909E-04 2.2353172E-02 at 110iterations 3.2270825E-04 1.1189461E-02 at 120iterations finished qdiffx linear iterations at : 15:40:38 total time elapsed so far: 7.030000 # loops : 120 mean,max change (kT/e) : 3.2270825E-04 1.1189461E-02 energy calculations done at 7.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.210000 DelPhi exited at 15:40:38 7.209u 0.174s 0:07.70 95.7% 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 15:40:38 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 = 5672 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 2.257515 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): 67.35700 138.3200 ymin,ymax (A): -6.168000 57.04100 zmin,zma (A): -3.345000 66.68100 x,y,z range (A): 70.96299 63.20900 70.02600 scale (grids/A): 2.257515 object centre (A): 102.8385 25.43650 31.66800 number of atom coordinates read : 5672 total number of charged atoms : 5501 net assigned charge : -2.499966 assigned positive charge : 866.7610 centred at (gu) : 89.13525 93.78471 89.76640 assigned negative charge : -869.2690 centred at (gu) : 89.41309 93.50027 90.22845 start vw surface at 0.2600000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 232745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44899 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 103328 mr = 173036 m= 25864 mr = 81653 m= 3440 mr = 19044 m= 166 mr = 2134 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 12468 time to turn everything in is 1.620000 number of dielectric boundary points 89624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 43867 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) : 1.505010 object centre at (A) : 102.8385 25.43650 31.66800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4966117E-02 0.2084676 midg,1,midg; midg,igrid,midg -0.2096450 0.2015217 1,midg,midg; igrid,midg,midg -0.5314796 0.1442977 gauss-seidel spectral radius is 0.9991701 estimated iterations to convergence 274 setup time was (sec) 1.920000 now iterating at: 15:40:40 rms-change max change #iterations 11.00628 316.6979 at 10iterations 6.282894 162.5084 at 20iterations 3.559895 73.01781 at 30iterations 2.011032 40.46513 at 40iterations 1.132302 21.84997 at 50iterations 0.6359684 13.85603 at 60iterations 0.3561257 7.233302 at 70iterations 0.1991829 3.686385 at 80iterations 0.1116486 1.875946 at 90iterations 6.2207136E-02 1.106236 at 100iterations 3.4702368E-02 0.6210489 at 110iterations 1.9362530E-02 0.3540115 at 120iterations 1.0811022E-02 0.1960316 at 130iterations 6.0306615E-03 0.1075020 at 140iterations 3.3697085E-03 5.8018208E-02 at 150iterations 1.8826474E-03 3.4585953E-02 at 160iterations 1.0556275E-03 1.8846512E-02 at 170iterations 5.9823290E-04 1.0322571E-02 at 180iterations finished qdiffx linear iterations at : 15:40:50 total time elapsed so far: 11.79000 # loops : 180 mean,max change (kT/e) : 5.9823290E-04 1.0322571E-02 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.96000 DelPhi exited at 15:40:51 11.967u 0.161s 0:12.53 96.7% 0+0k 0+0io 0pf+0w