Tue Oct 11 06:50:21 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 Tue Oct 11 2011 at 06:50:21 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2985 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 0.5442510 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): -20.11900 45.29200 ymin,ymax (A): 19.50100 76.76500 zmin,zma (A): -70.33700 -20.48100 x,y,z range (A): 65.41100 57.26400 49.85600 scale (grids/A): 0.5442510 object centre (A): 12.58650 48.13300 -45.40900 number of atom coordinates read : 2985 total number of charged atoms : 2838 net assigned charge : -4.040988 assigned positive charge : 436.5305 centred at (gu) : 89.57410 89.46247 89.80213 assigned negative charge : -440.5721 centred at (gu) : 89.56261 89.62466 89.81777 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5718 nv = 96 ne = 84 npr = 61981 no. pairs analyzed = 61981 no. exposed pairs = 3744 no. arc points = 26437 no. surface atoms = 1269 nbur = 1716 mkacc time = 0.1300000 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 = 1.596000 m= 245 mr = 2955 m= 0 mr = 11 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2997 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2646 ## 326 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7452 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5056281E-10 -3.2106381E-10 midg,1,midg; midg,igrid,midg 8.5098462E-10 -1.1039821E-09 1,midg,midg; igrid,midg,midg -3.4535919E-10 -1.5314228E-10 gauss-seidel spectral radius is 0.9825989 estimated iterations to convergence 62 setup time was (sec) 0.5600000 now iterating at: 06:50:22 rms-change max change #iterations 7.3046356E-02 12.35853 at 10iterations 4.9849586E-03 0.7997274 at 20iterations 3.2108225E-04 5.4603577E-02 at 30iterations 2.1534739E-05 4.0321350E-03 at 40iterations 1.4785800E-06 2.3841858E-04 at 50iterations finished qdiffx linear iterations at : 06:50:24 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 1.4785800E-06 2.3841858E-04 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 06:50:25 3.347u 0.202s 0:03.93 90.0% 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 Tue Oct 11 2011 at 06:50:25 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2985 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.632753 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): -20.11900 45.29200 ymin,ymax (A): 19.50100 76.76500 zmin,zma (A): -70.33700 -20.48100 x,y,z range (A): 65.41100 57.26400 49.85600 scale (grids/A): 1.632753 object centre (A): 12.58650 48.13300 -45.40900 number of atom coordinates read : 2985 total number of charged atoms : 2838 net assigned charge : -4.040988 assigned positive charge : 436.5305 centred at (gu) : 88.72147 88.38712 89.40591 assigned negative charge : -440.5721 centred at (gu) : 88.68751 88.87359 89.45284 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63175 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26437 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19782 mr = 42373 m= 2173 mr = 13799 m= 51 mr = 1053 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 27954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 283 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 21777 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) : 0.5442510 object centre at (A) : 12.58650 48.13300 -45.40900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9152816E-03 7.5947121E-03 midg,1,midg; midg,igrid,midg -1.0219151E-03 -4.3644634E-04 1,midg,midg; igrid,midg,midg 2.2838048E-03 -3.1883787E-02 gauss-seidel spectral radius is 0.9981918 estimated iterations to convergence 187 setup time was (sec) 0.7500000 now iterating at: 06:50:26 rms-change max change #iterations 3.295111 152.1232 at 10iterations 1.374690 55.52997 at 20iterations 0.5739961 21.97358 at 30iterations 0.2388018 9.605223 at 40iterations 0.1001571 3.810129 at 50iterations 4.1726589E-02 1.411634 at 60iterations 1.7453270E-02 0.6346912 at 70iterations 7.2874390E-03 0.2661166 at 80iterations 3.0501334E-03 0.1118488 at 90iterations 1.2743074E-03 4.3586731E-02 at 100iterations 5.3387205E-04 1.9447327E-02 at 110iterations 2.2213202E-04 7.8732967E-03 at 120iterations finished qdiffx linear iterations at : 06:50:32 total time elapsed so far: 7.110000 # loops : 120 mean,max change (kT/e) : 2.2213202E-04 7.8732967E-03 energy calculations done at 7.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 06:50:33 7.291u 0.206s 0:07.89 94.9% 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 Tue Oct 11 2011 at 06:50:33 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2985 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.449130 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): -20.11900 45.29200 ymin,ymax (A): 19.50100 76.76500 zmin,zma (A): -70.33700 -20.48100 x,y,z range (A): 65.41100 57.26400 49.85600 scale (grids/A): 2.449130 object centre (A): 12.58650 48.13300 -45.40900 number of atom coordinates read : 2985 total number of charged atoms : 2838 net assigned charge : -4.040988 assigned positive charge : 436.5305 centred at (gu) : 88.08203 87.58055 89.10860 assigned negative charge : -440.5721 centred at (gu) : 88.03108 88.31020 89.17919 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 146491 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26437 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67755 mr = 103549 m= 20035 mr = 53857 m= 3347 mr = 15180 m= 205 mr = 2157 m= 2 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.5999999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 63009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 22675 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) : 1.632753 object centre at (A) : 12.58650 48.13300 -45.40900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5307448E-02 0.1839984 midg,1,midg; midg,igrid,midg -1.1522481E-02 3.5029635E-02 1,midg,midg; igrid,midg,midg 6.5221251E-03 -0.6414564 gauss-seidel spectral radius is 0.9991430 estimated iterations to convergence 270 setup time was (sec) 1.390000 now iterating at: 06:50:34 rms-change max change #iterations 8.498361 299.1967 at 10iterations 4.758504 134.5090 at 20iterations 2.650434 60.59070 at 30iterations 1.470070 33.77972 at 40iterations 0.8151155 18.85565 at 50iterations 0.4491962 9.151020 at 60iterations 0.2487083 5.337978 at 70iterations 0.1368039 3.018845 at 80iterations 7.5398110E-02 1.672417 at 90iterations 4.1575469E-02 0.8861461 at 100iterations 2.2804286E-02 0.4424963 at 110iterations 1.2561098E-02 0.2585735 at 120iterations 6.9115032E-03 0.1430893 at 130iterations 3.8062178E-03 7.7838898E-02 at 140iterations 2.0926162E-03 4.3334484E-02 at 150iterations 1.1504616E-03 2.5310516E-02 at 160iterations 6.3174980E-04 1.3566017E-02 at 170iterations 3.4715584E-04 7.5054169E-03 at 180iterations finished qdiffx linear iterations at : 06:50:44 total time elapsed so far: 11.48000 # loops : 180 mean,max change (kT/e) : 3.4715584E-04 7.5054169E-03 energy calculations done at 11.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.67000 DelPhi exited at 06:50:45 11.674u 0.220s 0:12.33 96.4% 0+0k 0+0io 0pf+0w