Mon Oct 10 19:41:40 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 19:41:41 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4662 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5112078 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): -18.52400 36.80000 ymin,ymax (A): -30.42400 31.50500 zmin,zma (A): -3.892000 65.74700 x,y,z range (A): 55.32401 61.92900 69.63900 scale (grids/A): 0.5112078 object centre (A): 9.138001 0.5404997 30.92750 number of atom coordinates read : 4662 total number of charged atoms : 4413 net assigned charge : 9.206048 assigned positive charge : 698.8527 centred at (gu) : 90.33192 90.82731 88.16807 assigned negative charge : -689.6511 centred at (gu) : 90.21931 90.90438 88.12247 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7702 nv = 96 ne = 84 npr = 94037 no. pairs analyzed = 94037 no. exposed pairs = 6000 no. arc points = 41413 no. surface atoms = 2012 nbur = 2650 mkacc time = 0.2000000 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= 277 mr = 3955 m= 0 mr = 5 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4019 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3949 ## 606 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10238 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7470391E-11 1.5753941E-10 midg,1,midg; midg,igrid,midg 2.6749403E-10 -7.9279382E-11 1,midg,midg; igrid,midg,midg -1.4168768E-10 4.5913565E-10 gauss-seidel spectral radius is 0.9804236 estimated iterations to convergence 59 setup time was (sec) 0.6400000 now iterating at: 19:41:41 rms-change max change #iterations 6.7725547E-02 10.88843 at 10iterations 4.2742081E-03 0.6184769 at 20iterations 7.1774347E-04 9.6653223E-02 at 30iterations 2.6344619E-04 3.8861752E-02 at 40iterations 1.0443049E-04 1.5641212E-02 at 50iterations finished qdiffx linear iterations at : 19:41:44 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 1.0443049E-04 1.5641212E-02 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 19:41:45 3.675u 0.154s 0:04.22 90.5% 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 19:41:45 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4662 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.533623 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): -18.52400 36.80000 ymin,ymax (A): -30.42400 31.50500 zmin,zma (A): -3.892000 65.74700 x,y,z range (A): 55.32401 61.92900 69.63900 scale (grids/A): 1.533623 object centre (A): 9.138001 0.5404997 30.92750 number of atom coordinates read : 4662 total number of charged atoms : 4413 net assigned charge : 9.206048 assigned positive charge : 698.8527 centred at (gu) : 90.99426 92.48067 84.50288 assigned negative charge : -689.6511 centred at (gu) : 90.65787 92.71300 84.36698 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 86678 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41413 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25082 mr = 58956 m= 2255 mr = 16676 m= 47 mr = 962 m= 0 mr = 3 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 92 time to turn everything in is 0.5800000 number of dielectric boundary points 37465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 574 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 33246 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) : 0.5112078 object centre at (A) : 9.138001 0.5404997 30.92750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9499515E-03 2.0642484E-02 midg,1,midg; midg,igrid,midg 1.0195714E-02 -1.3108603E-02 1,midg,midg; igrid,midg,midg -9.2569826E-04 1.2875724E-02 gauss-seidel spectral radius is 0.9981077 estimated iterations to convergence 183 setup time was (sec) 0.8500000 now iterating at: 19:41:46 rms-change max change #iterations 3.773642 178.2062 at 10iterations 1.544768 57.01490 at 20iterations 0.6333807 23.24791 at 30iterations 0.2596420 8.235495 at 40iterations 0.1063985 3.600735 at 50iterations 4.3700974E-02 1.472271 at 60iterations 1.7969996E-02 0.5898039 at 70iterations 7.4362569E-03 0.2366581 at 80iterations 3.1226419E-03 0.1029596 at 90iterations 1.3514974E-03 5.7991028E-02 at 100iterations 6.3800981E-04 2.4034500E-02 at 110iterations 3.4543878E-04 1.2844086E-02 at 120iterations finished qdiffx linear iterations at : 19:41:52 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 3.4543878E-04 1.2844086E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.040000 DelPhi exited at 19:41:52 7.042u 0.153s 0:07.61 94.4% 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 19:41:52 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4662 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.300435 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): -18.52400 36.80000 ymin,ymax (A): -30.42400 31.50500 zmin,zma (A): -3.892000 65.74700 x,y,z range (A): 55.32401 61.92900 69.63900 scale (grids/A): 2.300435 object centre (A): 9.138001 0.5404997 30.92750 number of atom coordinates read : 4662 total number of charged atoms : 4413 net assigned charge : 9.206048 assigned positive charge : 698.8527 centred at (gu) : 91.49102 93.72061 81.75386 assigned negative charge : -689.6511 centred at (gu) : 90.98669 94.06946 81.55044 start vw surface at 0.1900000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 201889 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41413 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 90131 mr = 145109 m= 22853 mr = 70224 m= 3238 mr = 16317 m= 164 mr = 1984 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 327 time to turn everything in is 1.400000 number of dielectric boundary points 84584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 35213 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) : 1.533623 object centre at (A) : 9.138001 0.5404997 30.92750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1592640 0.4705032 midg,1,midg; midg,igrid,midg 0.1396560 -0.2964314 1,midg,midg; igrid,midg,midg -1.4336362E-02 0.1841753 gauss-seidel spectral radius is 0.9991605 estimated iterations to convergence 273 setup time was (sec) 1.670000 now iterating at: 19:41:54 rms-change max change #iterations 10.13495 271.2365 at 10iterations 5.802606 124.5610 at 20iterations 3.296767 85.18777 at 30iterations 1.862394 41.38563 at 40iterations 1.051103 24.28052 at 50iterations 0.5892847 12.65972 at 60iterations 0.3307327 7.202911 at 70iterations 0.1848147 3.682155 at 80iterations 0.1031590 2.073138 at 90iterations 5.7413731E-02 1.187922 at 100iterations 3.2053649E-02 0.6643867 at 110iterations 1.7813722E-02 0.4059105 at 120iterations 9.8931491E-03 0.2069817 at 130iterations 5.5099679E-03 0.1074109 at 140iterations 3.0694392E-03 5.8461189E-02 at 150iterations 1.7055001E-03 3.8892746E-02 at 160iterations 9.5273828E-04 1.7431259E-02 at 170iterations 5.3484627E-04 9.9048615E-03 at 180iterations finished qdiffx linear iterations at : 19:42:04 total time elapsed so far: 11.18000 # loops : 180 mean,max change (kT/e) : 5.3484627E-04 9.9048615E-03 energy calculations done at 11.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.35000 DelPhi exited at 19:42:04 11.352u 0.202s 0:11.84 97.5% 0+0k 0+0io 0pf+0w