Mon Oct 10 17:11:28 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 17:11:28 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2980 !!! WARNING: HIR 148 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: 0.5410334 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): -30.92400 34.87600 ymin,ymax (A): -22.53800 24.72200 zmin,zma (A): -7.310000 38.40500 x,y,z range (A): 65.80000 47.26000 45.71500 scale (grids/A): 0.5410334 object centre (A): 1.976002 1.092000 15.54750 number of atom coordinates read : 2980 total number of charged atoms : 2839 net assigned charge : -3.485973 assigned positive charge : 447.6550 centred at (gu) : 90.63430 90.27932 89.81999 assigned negative charge : -451.1421 centred at (gu) : 90.71732 90.16525 89.73653 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5625 nv = 96 ne = 84 npr = 59792 no. pairs analyzed = 59792 no. exposed pairs = 3900 no. arc points = 27487 no. surface atoms = 1302 nbur = 1678 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 = 1.596000 m= 222 mr = 2796 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.4100000 number of dielectric boundary points 3044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2732 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 7391 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.7758948E-10 2.7353886E-10 midg,1,midg; midg,igrid,midg -7.6747309E-10 4.8772253E-10 1,midg,midg; igrid,midg,midg 2.4098526E-10 -7.5676271E-10 gauss-seidel spectral radius is 0.9823933 estimated iterations to convergence 62 setup time was (sec) 0.7400000 now iterating at: 17:11:29 rms-change max change #iterations 6.9557086E-02 10.93040 at 10iterations 4.4921311E-03 0.7140646 at 20iterations 2.8800539E-04 4.9654007E-02 at 30iterations 1.9267885E-05 3.2539368E-03 at 40iterations 1.2910070E-06 2.2840500E-04 at 50iterations finished qdiffx linear iterations at : 17:11:33 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 1.2910070E-06 2.2840500E-04 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.520000 DelPhi exited at 17:11:33 4.528u 0.398s 0:05.28 92.9% 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 Mon Oct 10 2011 at 17:11:33 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2980 !!! WARNING: HIR 148 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: 1.623100 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): -30.92400 34.87600 ymin,ymax (A): -22.53800 24.72200 zmin,zma (A): -7.310000 38.40500 x,y,z range (A): 65.80000 47.26000 45.71500 scale (grids/A): 1.623100 object centre (A): 1.976002 1.092000 15.54750 number of atom coordinates read : 2980 total number of charged atoms : 2839 net assigned charge : -3.485973 assigned positive charge : 447.6550 centred at (gu) : 91.90207 90.83700 89.45940 assigned negative charge : -451.1421 centred at (gu) : 92.15160 90.49569 89.20942 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 62161 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27487 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18628 mr = 41034 m= 1865 mr = 12525 m= 53 mr = 827 m= 0 mr = 3 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 502 time to turn everything in is 0.6300000 number of dielectric boundary points 28318 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 345 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21706 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) : 0.5410334 object centre at (A) : 1.976002 1.092000 15.54750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7513766E-03 3.9681946E-03 midg,1,midg; midg,igrid,midg -1.4483307E-02 6.0247667E-03 1,midg,midg; igrid,midg,midg -1.1027022E-03 -2.1288641E-02 gauss-seidel spectral radius is 0.9981619 estimated iterations to convergence 185 setup time was (sec) 0.9500000 now iterating at: 17:11:35 rms-change max change #iterations 3.279167 155.5992 at 10iterations 1.345162 56.47989 at 20iterations 0.5573276 20.33255 at 30iterations 0.2307612 8.002716 at 40iterations 9.5470317E-02 3.239163 at 50iterations 3.9478369E-02 1.496292 at 60iterations 1.6405439E-02 0.6095009 at 70iterations 6.8060649E-03 0.3006668 at 80iterations 2.8115714E-03 0.1007252 at 90iterations 1.1727036E-03 4.3930054E-02 at 100iterations 4.8400456E-04 1.7908096E-02 at 110iterations 2.0236486E-04 7.0072412E-03 at 120iterations finished qdiffx linear iterations at : 17:11:44 total time elapsed so far: 9.730000 # loops : 120 mean,max change (kT/e) : 2.0236486E-04 7.0072412E-03 energy calculations done at 9.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.940000 DelPhi exited at 17:11:44 9.942u 0.455s 0:10.83 95.9% 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 Mon Oct 10 2011 at 17:11:44 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2980 !!! WARNING: HIR 148 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: 2.434650 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): -30.92400 34.87600 ymin,ymax (A): -22.53800 24.72200 zmin,zma (A): -7.310000 38.40500 x,y,z range (A): 65.80000 47.26000 45.71500 scale (grids/A): 2.434650 object centre (A): 1.976002 1.092000 15.54750 number of atom coordinates read : 2980 total number of charged atoms : 2839 net assigned charge : -3.485973 assigned positive charge : 447.6550 centred at (gu) : 92.85297 91.25528 89.18876 assigned negative charge : -451.1421 centred at (gu) : 93.22716 90.74337 88.81400 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 144166 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27487 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 64916 mr = 100697 m= 18032 mr = 50484 m= 2759 mr = 13269 m= 172 mr = 1652 m= 0 mr = 78 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 1815 time to turn everything in is 1.590000 number of dielectric boundary points 63865 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 22685 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) : 1.623100 object centre at (A) : 1.976002 1.092000 15.54750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3113131E-02 6.1839163E-02 midg,1,midg; midg,igrid,midg -0.2075784 0.1163100 1,midg,midg; igrid,midg,midg 0.2272644 -0.5154366 gauss-seidel spectral radius is 0.9991347 estimated iterations to convergence 269 setup time was (sec) 1.960000 now iterating at: 17:11:47 rms-change max change #iterations 8.629238 357.9098 at 10iterations 4.839621 136.1523 at 20iterations 2.685064 61.97429 at 30iterations 1.491731 41.81209 at 40iterations 0.8263952 17.38323 at 50iterations 0.4547634 9.669802 at 60iterations 0.2504852 5.389338 at 70iterations 0.1381253 3.301945 at 80iterations 7.5894229E-02 1.588022 at 90iterations 4.1632846E-02 0.8904953 at 100iterations 2.2824921E-02 0.4990311 at 110iterations 1.2536523E-02 0.2707825 at 120iterations 6.8740183E-03 0.1345787 at 130iterations 3.7747102E-03 8.0701828E-02 at 140iterations 2.0659503E-03 4.6109438E-02 at 150iterations 1.1380216E-03 2.6306152E-02 at 160iterations 6.2175281E-04 1.3555288E-02 at 170iterations 3.4096843E-04 7.0953369E-03 at 180iterations finished qdiffx linear iterations at : 17:12:02 total time elapsed so far: 17.47000 # loops : 180 mean,max change (kT/e) : 3.4096843E-04 7.0953369E-03 energy calculations done at 17.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.68000 DelPhi exited at 17:12:03 17.689u 0.458s 0:18.47 98.1% 0+0k 0+0io 0pf+0w