Wed Dec 21 14:21:36 PST 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 Wed Dec 21 2011 at 14:21:37 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5992761 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): -24.42500 34.98000 ymin,ymax (A): -19.65300 20.73300 zmin,zma (A): -2.867000 38.74400 x,y,z range (A): 59.40500 40.38600 41.61100 scale (grids/A): 0.5992761 object centre (A): 5.277502 0.5400000 17.93850 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 267.0744 centred at (gu) : 89.78074 90.36520 90.26155 assigned negative charge : -289.0263 centred at (gu) : 89.77446 90.46644 90.40583 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4810 nv = 96 ne = 84 npr = 39689 no. pairs analyzed = 39689 no. exposed pairs = 2394 no. arc points = 17086 no. surface atoms = 808 nbur = 1156 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 203 mr = 2647 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.1800000 number of dielectric boundary points 2359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1632 ## 133 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 5700 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0993632E-09 -1.3847408E-08 midg,1,midg; midg,igrid,midg -6.0113052E-09 -1.2891498E-08 1,midg,midg; igrid,midg,midg -9.7891899E-09 -8.5718366E-09 gauss-seidel spectral radius is 0.9855374 estimated iterations to convergence 68 setup time was (sec) 0.4000000 now iterating at: 14:21:38 rms-change max change #iterations 9.7456731E-02 17.90296 at 10iterations 8.2602734E-03 1.433070 at 20iterations 6.8780949E-04 0.1166458 at 30iterations 5.8956030E-05 1.0429382E-02 at 40iterations 4.9361493E-06 9.5129013E-04 at 50iterations finished qdiffx linear iterations at : 14:21:41 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 4.9361493E-06 9.5129013E-04 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 14:21:54 3.710u 0.222s 0:18.79 20.9% 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 Wed Dec 21 2011 at 14:21:58 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.797828 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): -24.42500 34.98000 ymin,ymax (A): -19.65300 20.73300 zmin,zma (A): -2.867000 38.74400 x,y,z range (A): 59.40500 40.38600 41.61100 scale (grids/A): 1.797828 object centre (A): 5.277502 0.5400000 17.93850 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 267.0744 centred at (gu) : 89.34235 91.09560 90.78506 assigned negative charge : -289.0263 centred at (gu) : 89.32329 91.39954 91.21773 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 52524 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17086 grid for indexing accessible points = 1.400000 m= 18693 mr = 36236 m= 2318 mr = 14242 m= 67 mr = 1438 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 563 time to turn everything in is 0.2600000 number of dielectric boundary points 21672 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 13799 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) : 0.5992761 object centre at (A) : 5.277502 0.5400000 17.93850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5022443E-03 -3.1979106E-02 midg,1,midg; midg,igrid,midg -1.4238035E-02 -2.9364334E-02 1,midg,midg; igrid,midg,midg -2.0596609E-02 -2.5374085E-02 gauss-seidel spectral radius is 0.9983946 estimated iterations to convergence 198 setup time was (sec) 0.4800000 now iterating at: 14:21:59 rms-change max change #iterations 3.201779 143.8402 at 10iterations 1.406412 54.54778 at 20iterations 0.6176419 21.55727 at 30iterations 0.2709031 10.84536 at 40iterations 0.1184494 4.555649 at 50iterations 5.2220974E-02 1.906866 at 60iterations 2.2877483E-02 0.8869705 at 70iterations 1.0011957E-02 0.3946991 at 80iterations 4.4124289E-03 0.1724815 at 90iterations 1.9327316E-03 7.5185776E-02 at 100iterations 8.4942661E-04 3.2531738E-02 at 110iterations 3.7414243E-04 1.5415192E-02 at 120iterations finished qdiffx linear iterations at : 14:22:09 total time elapsed so far: 10.03000 # loops : 120 mean,max change (kT/e) : 3.7414243E-04 1.5415192E-02 energy calculations done at 10.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.17000 DelPhi exited at 14:22:22 10.169u 0.229s 0:24.34 42.6% 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 Wed Dec 21 2011 at 14:22:24 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.696743 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): -24.42500 34.98000 ymin,ymax (A): -19.65300 20.73300 zmin,zma (A): -2.867000 38.74400 x,y,z range (A): 59.40500 40.38600 41.61100 scale (grids/A): 2.696743 object centre (A): 5.277502 0.5400000 17.93850 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 267.0744 centred at (gu) : 89.01366 91.64339 91.17773 assigned negative charge : -289.0263 centred at (gu) : 88.98501 92.09940 91.82669 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 121346 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17086 grid for indexing accessible points = 1.400000 m= 61601 mr = 87601 m= 20722 mr = 51261 m= 3928 mr = 16976 m= 296 mr = 2963 m= 5 mr = 173 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 2093 time to turn everything in is 0.6800000 number of dielectric boundary points 48924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 14112 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) : 1.797828 object centre at (A) : 5.277502 0.5400000 17.93850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6457309E-02 -0.3432520 midg,1,midg; midg,igrid,midg -0.1509339 -0.3291751 1,midg,midg; igrid,midg,midg -0.1851574 -0.3165268 gauss-seidel spectral radius is 0.9991726 estimated iterations to convergence 275 setup time was (sec) 0.9500000 now iterating at: 14:22:26 rms-change max change #iterations 7.725729 273.3754 at 10iterations 4.371076 126.4870 at 20iterations 2.446447 67.73559 at 30iterations 1.361568 34.88618 at 40iterations 0.7579334 19.34513 at 50iterations 0.4225268 11.02438 at 60iterations 0.2353971 5.552438 at 70iterations 0.1304981 2.864723 at 80iterations 7.2298937E-02 1.610180 at 90iterations 4.0212598E-02 0.8697205 at 100iterations 2.2319030E-02 0.4755900 at 110iterations 1.2399869E-02 0.2723045 at 120iterations 6.8774447E-03 0.1494884 at 130iterations 3.8227122E-03 8.3291054E-02 at 140iterations 2.1148233E-03 4.5475006E-02 at 150iterations 1.1762375E-03 2.5753021E-02 at 160iterations 6.5178331E-04 1.4315605E-02 at 170iterations 3.6317843E-04 8.2058907E-03 at 180iterations finished qdiffx linear iterations at : 14:22:40 total time elapsed so far: 15.24000 # loops : 180 mean,max change (kT/e) : 3.6317843E-04 8.2058907E-03 energy calculations done at 15.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.37000 DelPhi exited at 14:22:43 15.367u 0.326s 0:19.99 78.4% 0+0k 0+0io 0pf+0w