Tue Oct 11 06:58:51 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 06:58:51 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2981 !!! 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: 0.5609833 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): -19.44500 44.01500 ymin,ymax (A): 19.58000 74.66600 zmin,zma (A): -70.06200 -21.09600 x,y,z range (A): 63.46000 55.08600 48.96600 scale (grids/A): 0.5609833 object centre (A): 12.28500 47.12300 -45.57900 number of atom coordinates read : 2981 total number of charged atoms : 2836 net assigned charge : -1.054985 assigned positive charge : 437.5715 centred at (gu) : 89.85643 90.24259 89.87554 assigned negative charge : -438.6271 centred at (gu) : 89.84367 90.41340 89.88303 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6078 nv = 96 ne = 84 npr = 61772 no. pairs analyzed = 61772 no. exposed pairs = 3773 no. arc points = 26810 no. surface atoms = 1275 nbur = 1706 mkacc time = 0.2100000 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 = 1.540000 m= 274 mr = 3159 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2615 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 7813 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5137873E-11 -1.8846516E-10 midg,1,midg; midg,igrid,midg 1.6824027E-09 -2.2137376E-09 1,midg,midg; igrid,midg,midg -2.6306754E-10 3.3699512E-11 gauss-seidel spectral radius is 0.9836106 estimated iterations to convergence 64 setup time was (sec) 0.8000000 now iterating at: 06:58:52 rms-change max change #iterations 8.6127974E-02 14.86179 at 10iterations 6.1344835E-03 0.9614964 at 20iterations 4.9662642E-04 8.4753990E-02 at 30iterations 6.2118423E-05 1.4707565E-02 at 40iterations 1.2273363E-05 3.2520294E-03 at 50iterations finished qdiffx linear iterations at : 06:58:56 total time elapsed so far: 4.680000 # loops : 50 mean,max change (kT/e) : 1.2273363E-05 3.2520294E-03 energy calculations done at 4.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.890000 DelPhi exited at 06:58:56 4.890u 0.445s 0:05.64 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 Tue Oct 11 2011 at 06:58:57 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2981 !!! 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.682950 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): -19.44500 44.01500 ymin,ymax (A): 19.58000 74.66600 zmin,zma (A): -70.06200 -21.09600 x,y,z range (A): 63.46000 55.08600 48.96600 scale (grids/A): 1.682950 object centre (A): 12.28500 47.12300 -45.57900 number of atom coordinates read : 2981 total number of charged atoms : 2836 net assigned charge : -1.054985 assigned positive charge : 437.5715 centred at (gu) : 89.56861 90.72699 89.62619 assigned negative charge : -438.6271 centred at (gu) : 89.53036 91.24003 89.64867 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 65703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26810 grid for indexing accessible points = 1.400000 m= 22635 mr = 43656 m= 2885 mr = 16260 m= 78 mr = 1662 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 29723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 226 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 21839 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) : 0.5609833 object centre at (A) : 12.28500 47.12300 -45.57900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2223123E-03 1.0881736E-02 midg,1,midg; midg,igrid,midg 2.2271466E-03 -2.5170457E-03 1,midg,midg; igrid,midg,midg 7.8906417E-03 -1.4904904E-02 gauss-seidel spectral radius is 0.9983015 estimated iterations to convergence 193 setup time was (sec) 1.050000 now iterating at: 06:58:58 rms-change max change #iterations 3.528145 172.2409 at 10iterations 1.513312 58.16285 at 20iterations 0.6467759 25.03538 at 30iterations 0.2780234 11.88608 at 40iterations 0.1192798 4.302135 at 50iterations 5.1438726E-02 2.044456 at 60iterations 2.1978762E-02 0.8416195 at 70iterations 9.4440607E-03 0.3216438 at 80iterations 4.0587159E-03 0.1346452 at 90iterations 1.7460630E-03 6.0036659E-02 at 100iterations 7.5361092E-04 2.5863647E-02 at 110iterations 3.2621561E-04 1.1810303E-02 at 120iterations finished qdiffx linear iterations at : 06:59:08 total time elapsed so far: 11.18000 # loops : 120 mean,max change (kT/e) : 3.2621561E-04 1.1810303E-02 energy calculations done at 11.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 06:59:09 11.790u 0.486s 0:12.98 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 Tue Oct 11 2011 at 06:59:10 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2981 !!! 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: 2.524425 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): -19.44500 44.01500 ymin,ymax (A): 19.58000 74.66600 zmin,zma (A): -70.06200 -21.09600 x,y,z range (A): 63.46000 55.08600 48.96600 scale (grids/A): 2.524425 object centre (A): 12.28500 47.12300 -45.57900 number of atom coordinates read : 2981 total number of charged atoms : 2836 net assigned charge : -1.054985 assigned positive charge : 437.5715 centred at (gu) : 89.35271 91.09032 89.43909 assigned negative charge : -438.6271 centred at (gu) : 89.29552 91.85980 89.47291 start vw surface at 0.1900000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 152019 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26810 grid for indexing accessible points = 1.400000 m= 73940 mr = 106408 m= 25296 mr = 59375 m= 4862 mr = 20043 m= 378 mr = 3425 m= 6 mr = 178 m= 1 mr = 0 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.870000 number of dielectric boundary points 67074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 22661 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) : 1.682950 object centre at (A) : 12.28500 47.12300 -45.57900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1124522 0.2233912 midg,1,midg; midg,igrid,midg 1.4546671E-02 -3.3803958E-02 1,midg,midg; igrid,midg,midg 0.1148220 -7.0768587E-02 gauss-seidel spectral radius is 0.9991761 estimated iterations to convergence 275 setup time was (sec) 2.230000 now iterating at: 06:59:12 rms-change max change #iterations 8.902784 363.5420 at 10iterations 5.050942 138.7220 at 20iterations 2.845300 68.14207 at 30iterations 1.600627 35.76078 at 40iterations 0.8972539 17.77331 at 50iterations 0.5038414 10.99820 at 60iterations 0.2814721 6.340901 at 70iterations 0.1567173 3.362986 at 80iterations 8.7650836E-02 1.769835 at 90iterations 4.8788674E-02 0.9822083 at 100iterations 2.7254699E-02 0.5833092 at 110iterations 1.5144809E-02 0.3193507 at 120iterations 8.4424037E-03 0.1705494 at 130iterations 4.7017955E-03 0.1053581 at 140iterations 2.6201473E-03 4.9723148E-02 at 150iterations 1.4580988E-03 2.9739141E-02 at 160iterations 8.1469573E-04 1.7593384E-02 at 170iterations 4.5573572E-04 8.6942017E-03 at 180iterations finished qdiffx linear iterations at : 06:59:28 total time elapsed so far: 18.36000 # loops : 180 mean,max change (kT/e) : 4.5573572E-04 8.6942017E-03 energy calculations done at 18.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.59000 DelPhi exited at 06:59:29 18.592u 0.490s 0:19.72 96.7% 0+0k 0+0io 0pf+0w