Mon Oct 10 14:41:06 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 14:41:06 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5010 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: HIR 299 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5145476 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): -20.15300 49.03400 ymin,ymax (A): 10.36400 73.14500 zmin,zma (A): 33.63400 95.21400 x,y,z range (A): 69.18700 62.78100 61.58000 scale (grids/A): 0.5145476 object centre (A): 14.44050 41.75450 64.42400 number of atom coordinates read : 5010 total number of charged atoms : 4846 net assigned charge : 0.9340197 assigned positive charge : 753.9683 centred at (gu) : 90.23590 90.80652 90.16805 assigned negative charge : -753.0390 centred at (gu) : 90.23831 90.76250 90.17917 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8155 nv = 96 ne = 84 npr = 103980 no. pairs analyzed = 103980 no. exposed pairs = 6020 no. arc points = 39937 no. surface atoms = 2050 nbur = 2960 mkacc time = 0.2500000 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 = 1.652000 m= 303 mr = 4386 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3958 ## 513 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 11080 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8279887E-11 -2.2476456E-11 midg,1,midg; midg,igrid,midg -1.0381748E-10 1.9340431E-10 1,midg,midg; igrid,midg,midg 2.1021497E-11 7.1328117E-12 gauss-seidel spectral radius is 0.9806883 estimated iterations to convergence 59 setup time was (sec) 0.7400000 now iterating at: 14:41:07 rms-change max change #iterations 7.3709480E-02 10.46243 at 10iterations 5.0979811E-03 0.7925339 at 20iterations 1.1875960E-03 0.1821766 at 30iterations 4.9076584E-04 6.3381195E-02 at 40iterations 2.1685878E-04 2.8873444E-02 at 50iterations finished qdiffx linear iterations at : 14:41:10 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 2.1685878E-04 2.8873444E-02 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.790000 DelPhi exited at 14:41:11 3.790u 0.231s 0:04.32 93.0% 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 Mon Oct 10 2011 at 14:41:11 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5010 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: HIR 299 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.543643 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): -20.15300 49.03400 ymin,ymax (A): 10.36400 73.14500 zmin,zma (A): 33.63400 95.21400 x,y,z range (A): 69.18700 62.78100 61.58000 scale (grids/A): 1.543643 object centre (A): 14.44050 41.75450 64.42400 number of atom coordinates read : 5010 total number of charged atoms : 4846 net assigned charge : 0.9340197 assigned positive charge : 753.9683 centred at (gu) : 90.70621 92.41772 90.50276 assigned negative charge : -753.0390 centred at (gu) : 90.71423 92.28715 90.53687 start vw surface at 0.2200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 93118 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39937 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 27605 mr = 65720 m= 2504 mr = 18667 m= 41 mr = 1139 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 106 time to turn everything in is 0.7100000 number of dielectric boundary points 37742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 480 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 36520 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) : 0.5145476 object centre at (A) : 14.44050 41.75450 64.42400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2380855E-03 8.0854576E-03 midg,1,midg; midg,igrid,midg -7.3822439E-03 1.3610390E-04 1,midg,midg; igrid,midg,midg -2.6021108E-02 -5.3148107E-03 gauss-seidel spectral radius is 0.9981548 estimated iterations to convergence 185 setup time was (sec) 1.050000 now iterating at: 14:41:12 rms-change max change #iterations 3.967035 157.5959 at 10iterations 1.634862 55.80869 at 20iterations 0.6798127 21.12438 at 30iterations 0.2815333 8.754059 at 40iterations 0.1170285 3.505199 at 50iterations 4.8607759E-02 1.467163 at 60iterations 2.0446798E-02 0.6069164 at 70iterations 8.7470906E-03 0.2719326 at 80iterations 3.9710440E-03 0.1412792 at 90iterations 1.9899195E-03 5.9547424E-02 at 100iterations 1.1711619E-03 3.5022736E-02 at 110iterations 7.8724872E-04 2.0735741E-02 at 120iterations finished qdiffx linear iterations at : 14:41:20 total time elapsed so far: 8.960000 # loops : 120 mean,max change (kT/e) : 7.8724872E-04 2.0735741E-02 energy calculations done at 8.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.170000 DelPhi exited at 14:41:21 9.177u 0.223s 0:09.79 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 14:41:21 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5010 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: HIR 299 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.315464 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): -20.15300 49.03400 ymin,ymax (A): 10.36400 73.14500 zmin,zma (A): 33.63400 95.21400 x,y,z range (A): 69.18700 62.78100 61.58000 scale (grids/A): 2.315464 object centre (A): 14.44050 41.75450 64.42400 number of atom coordinates read : 5010 total number of charged atoms : 4846 net assigned charge : 0.9340197 assigned positive charge : 753.9683 centred at (gu) : 91.05880 93.62617 90.75371 assigned negative charge : -753.0390 centred at (gu) : 91.07124 93.43049 90.80539 start vw surface at 0.2100000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 217745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39937 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 98600 mr = 161547 m= 25622 mr = 77567 m= 3524 mr = 18935 m= 178 mr = 2257 m= 3 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 374 time to turn everything in is 1.660000 number of dielectric boundary points 85302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 38674 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) : 1.543643 object centre at (A) : 14.44050 41.75450 64.42400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0294656E-02 0.1469297 midg,1,midg; midg,igrid,midg -0.1564527 -1.4048696E-02 1,midg,midg; igrid,midg,midg -0.5441632 -2.1531476E-02 gauss-seidel spectral radius is 0.9991733 estimated iterations to convergence 275 setup time was (sec) 1.970000 now iterating at: 14:41:23 rms-change max change #iterations 10.69463 286.9600 at 10iterations 6.154191 149.1484 at 20iterations 3.522729 86.70893 at 30iterations 2.004740 45.27839 at 40iterations 1.137934 22.46246 at 50iterations 0.6425352 12.32812 at 60iterations 0.3628359 6.650036 at 70iterations 0.2038806 3.607861 at 80iterations 0.1145386 1.997886 at 90iterations 6.4268745E-02 1.129835 at 100iterations 3.6000442E-02 0.6196194 at 110iterations 2.0256070E-02 0.4365117 at 120iterations 1.1381423E-02 0.2074003 at 130iterations 6.4695063E-03 0.1165333 at 140iterations 3.7322803E-03 6.9175720E-02 at 150iterations 2.2156220E-03 4.1397095E-02 at 160iterations 1.3822841E-03 2.5569916E-02 at 170iterations 9.2393660E-04 1.5777588E-02 at 180iterations finished qdiffx linear iterations at : 14:41:33 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 9.2393660E-04 1.5777588E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 14:41:34 12.750u 0.202s 0:13.37 96.8% 0+0k 0+0io 0pf+0w