Mon Oct 10 14:10:35 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 14:10:35 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4114 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5058542 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): 4.118000 74.49400 ymin,ymax (A): 42.90300 105.9030 zmin,zma (A): -12.22500 52.26700 x,y,z range (A): 70.37601 63.00000 64.49200 scale (grids/A): 0.5058542 object centre (A): 39.30600 74.40300 20.02100 number of atom coordinates read : 4114 total number of charged atoms : 3964 net assigned charge : -1.499992 assigned positive charge : 626.0717 centred at (gu) : 90.53624 90.76436 93.38451 assigned negative charge : -627.5754 centred at (gu) : 90.58296 90.67272 93.39537 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6954 nv = 96 ne = 84 npr = 77430 no. pairs analyzed = 77430 no. exposed pairs = 5822 no. arc points = 41508 no. surface atoms = 1925 nbur = 2189 mkacc time = 0.2300000 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 = 1.680000 m= 252 mr = 3251 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 3955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4014 ## 627 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 9236 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7055948E-13 -9.1943751E-11 midg,1,midg; midg,igrid,midg -1.5187795E-10 1.8248734E-10 1,midg,midg; igrid,midg,midg 5.8552510E-11 -1.1876923E-10 gauss-seidel spectral radius is 0.9799853 estimated iterations to convergence 58 setup time was (sec) 0.7400000 now iterating at: 14:10:36 rms-change max change #iterations 5.8472704E-02 12.90927 at 10iterations 3.2003613E-03 0.5129147 at 20iterations 2.6417294E-04 4.8249245E-02 at 30iterations 5.0380939E-05 1.2744904E-02 at 40iterations 1.2747612E-05 3.5715103E-03 at 50iterations finished qdiffx linear iterations at : 14:10:39 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 1.2747612E-05 3.5715103E-03 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 14:10:40 4.239u 0.257s 0:05.10 87.8% 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 14:10:40 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4114 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.517563 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): 4.118000 74.49400 ymin,ymax (A): 42.90300 105.9030 zmin,zma (A): -12.22500 52.26700 x,y,z range (A): 70.37601 63.00000 64.49200 scale (grids/A): 1.517563 object centre (A): 39.30600 74.40300 20.02100 number of atom coordinates read : 4114 total number of charged atoms : 3964 net assigned charge : -1.499992 assigned positive charge : 626.0717 centred at (gu) : 91.60699 92.29155 100.1524 assigned negative charge : -627.5754 centred at (gu) : 91.74845 92.01777 100.1858 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 77556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41508 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22952 mr = 50186 m= 2027 mr = 14682 m= 37 mr = 795 m= 0 mr = 1 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 36908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 594 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 29663 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) : 0.5058542 object centre at (A) : 39.30600 74.40300 20.02100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4484842E-03 -1.8315263E-02 midg,1,midg; midg,igrid,midg -1.0786415E-02 1.0666966E-02 1,midg,midg; igrid,midg,midg 6.5542008E-03 -6.1576548E-03 gauss-seidel spectral radius is 0.9980165 estimated iterations to convergence 179 setup time was (sec) 1.020000 now iterating at: 14:10:42 rms-change max change #iterations 3.425905 150.0781 at 10iterations 1.368928 59.87088 at 20iterations 0.5460997 18.09825 at 30iterations 0.2189705 7.470757 at 40iterations 8.7682173E-02 3.194115 at 50iterations 3.4945045E-02 1.176386 at 60iterations 1.4066176E-02 0.4550047 at 70iterations 5.6418972E-03 0.2133265 at 80iterations 2.2725570E-03 7.6576233E-02 at 90iterations 9.2192809E-04 3.3363342E-02 at 100iterations 3.7791970E-04 1.2894988E-02 at 110iterations 1.5968701E-04 5.4311752E-03 at 120iterations finished qdiffx linear iterations at : 14:10:50 total time elapsed so far: 9.360000 # loops : 120 mean,max change (kT/e) : 1.5968701E-04 5.4311752E-03 energy calculations done at 9.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.540000 DelPhi exited at 14:10:51 9.543u 0.285s 0:10.39 94.5% 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 14:10:51 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4114 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.276344 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): 4.118000 74.49400 ymin,ymax (A): 42.90300 105.9030 zmin,zma (A): -12.22500 52.26700 x,y,z range (A): 70.37601 63.00000 64.49200 scale (grids/A): 2.276344 object centre (A): 39.30600 74.40300 20.02100 number of atom coordinates read : 4114 total number of charged atoms : 3964 net assigned charge : -1.499992 assigned positive charge : 626.0717 centred at (gu) : 92.41021 93.43678 105.2282 assigned negative charge : -627.5754 centred at (gu) : 92.62262 93.02657 105.2785 start vw surface at 0.2000000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 180469 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41508 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 80409 mr = 124152 m= 21107 mr = 60992 m= 2883 mr = 14857 m= 126 mr = 1660 m= 5 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.740000 number of dielectric boundary points 83300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 31621 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) : 1.517563 object centre at (A) : 39.30600 74.40300 20.02100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1289467 -0.5524945 midg,1,midg; midg,igrid,midg -0.1758396 0.2035437 1,midg,midg; igrid,midg,midg 0.1386519 -7.7950977E-02 gauss-seidel spectral radius is 0.9991165 estimated iterations to convergence 266 setup time was (sec) 2.070000 now iterating at: 14:10:53 rms-change max change #iterations 9.420474 287.2701 at 10iterations 5.372804 143.3939 at 20iterations 3.030804 72.61520 at 30iterations 1.694903 37.29033 at 40iterations 0.9453670 21.74537 at 50iterations 0.5242987 11.44977 at 60iterations 0.2898657 6.331973 at 70iterations 0.1601501 3.287323 at 80iterations 8.8101752E-02 2.027809 at 90iterations 4.8628125E-02 1.053539 at 100iterations 2.6688650E-02 0.5610514 at 110iterations 1.4633200E-02 0.3017130 at 120iterations 8.0345906E-03 0.1657944 at 130iterations 4.4148667E-03 9.0180874E-02 at 140iterations 2.4272262E-03 4.7679901E-02 at 150iterations 1.3355544E-03 2.8041840E-02 at 160iterations 7.4050273E-04 1.5343577E-02 at 170iterations 4.1425915E-04 8.2588196E-03 at 180iterations finished qdiffx linear iterations at : 14:11:07 total time elapsed so far: 15.88000 # loops : 180 mean,max change (kT/e) : 4.1425915E-04 8.2588196E-03 energy calculations done at 15.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.06000 DelPhi exited at 14:11:07 16.062u 0.302s 0:16.71 97.9% 0+0k 0+0io 0pf+0w