Sat Oct 8 14:33:52 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 Sat Oct 8 2011 at 14:33:53 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 0.6404606 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): -12.16200 43.42300 ymin,ymax (A): -22.80600 22.45200 zmin,zma (A): -7.571000 47.93800 x,y,z range (A): 55.58500 45.25800 55.50900 scale (grids/A): 0.6404606 object centre (A): 15.63050 -0.1770000 20.18350 number of atom coordinates read : 3040 total number of charged atoms : 2893 net assigned charge : -0.9859914 assigned positive charge : 456.3236 centred at (gu) : 88.80596 89.77255 91.53434 assigned negative charge : -457.3102 centred at (gu) : 88.78827 89.66939 91.46300 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8219 nv = 96 ne = 84 npr = 63529 no. pairs analyzed = 63529 no. exposed pairs = 3444 no. arc points = 24467 no. surface atoms = 1170 nbur = 1870 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 408 mr = 4771 m= 3 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3900000 number of dielectric boundary points 3805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2376 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10048 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.2780325E-09 1.1640965E-08 midg,1,midg; midg,igrid,midg -1.6816719E-08 1.1993713E-08 1,midg,midg; igrid,midg,midg -5.1685793E-09 6.8707379E-10 gauss-seidel spectral radius is 0.9874027 estimated iterations to convergence 73 setup time was (sec) 0.6800000 now iterating at: 14:33:53 rms-change max change #iterations 0.1558611 22.87955 at 10iterations 1.5488500E-02 2.211983 at 20iterations 1.5448224E-03 0.2154884 at 30iterations 1.5934836E-04 2.3180008E-02 at 40iterations 1.6898806E-05 2.0446777E-03 at 50iterations finished qdiffx linear iterations at : 14:33:57 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 1.6898806E-05 2.0446777E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 14:33:57 4.286u 0.271s 0:04.92 92.4% 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 Sat Oct 8 2011 at 14:33:57 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 1.921382 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): -12.16200 43.42300 ymin,ymax (A): -22.80600 22.45200 zmin,zma (A): -7.571000 47.93800 x,y,z range (A): 55.58500 45.25800 55.50900 scale (grids/A): 1.921382 object centre (A): 15.63050 -0.1770000 20.18350 number of atom coordinates read : 3040 total number of charged atoms : 2893 net assigned charge : -0.9859914 assigned positive charge : 456.3236 centred at (gu) : 86.41710 89.31679 94.60284 assigned negative charge : -457.3102 centred at (gu) : 86.36457 89.00787 94.38865 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 90271 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24467 grid for indexing accessible points = 1.400000 m= 32476 mr = 65184 m= 4637 mr = 24419 m= 262 mr = 2745 m= 3 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 492 time to turn everything in is 0.7800000 number of dielectric boundary points 35209 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 22805 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) : 0.6404606 object centre at (A) : 15.63050 -0.1770000 20.18350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3942841E-02 1.6031714E-02 midg,1,midg; midg,igrid,midg -8.3742961E-03 1.7831814E-02 1,midg,midg; igrid,midg,midg -3.9753176E-02 1.3631067E-02 gauss-seidel spectral radius is 0.9986947 estimated iterations to convergence 219 setup time was (sec) 1.100000 now iterating at: 14:33:59 rms-change max change #iterations 4.756164 207.1570 at 10iterations 2.268961 75.27628 at 20iterations 1.081922 33.23571 at 30iterations 0.5168440 14.73273 at 40iterations 0.2465738 7.265629 at 50iterations 0.1177586 3.499519 at 60iterations 5.6197681E-02 1.857586 at 70iterations 2.6825897E-02 0.7497864 at 80iterations 1.2790248E-02 0.3569221 at 90iterations 6.0948622E-03 0.1835403 at 100iterations 2.9132357E-03 7.9928160E-02 at 110iterations 1.3908858E-03 4.0742874E-02 at 120iterations finished qdiffx linear iterations at : 14:34:08 total time elapsed so far: 9.800000 # loops : 120 mean,max change (kT/e) : 1.3908858E-03 4.0742874E-02 energy calculations done at 9.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.980000 DelPhi exited at 14:34:08 9.985u 0.304s 0:10.76 95.5% 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 Sat Oct 8 2011 at 14:34:08 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 2.882072 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): -12.16200 43.42300 ymin,ymax (A): -22.80600 22.45200 zmin,zma (A): -7.571000 47.93800 x,y,z range (A): 55.58500 45.25800 55.50900 scale (grids/A): 2.882072 object centre (A): 15.63050 -0.1770000 20.18350 number of atom coordinates read : 3040 total number of charged atoms : 2893 net assigned charge : -0.9859914 assigned positive charge : 456.3236 centred at (gu) : 84.62551 88.97514 96.90388 assigned negative charge : -457.3102 centred at (gu) : 84.54690 88.51177 96.58302 start vw surface at 0.1800000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 209399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24467 grid for indexing accessible points = 1.400000 m= 106741 mr = 157705 m= 36907 mr = 88912 m= 8273 mr = 29752 m= 1162 mr = 5973 m= 72 mr = 785 m= 0 mr = 26 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 1548 time to turn everything in is 2.050000 number of dielectric boundary points 79401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.210000 number of grid points assigned charge 23139 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) : 1.921382 object centre at (A) : 15.63050 -0.1770000 20.18350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5026359E-02 0.2395747 midg,1,midg; midg,igrid,midg -6.6382177E-02 0.2094776 1,midg,midg; igrid,midg,midg -0.6031994 0.1897756 gauss-seidel spectral radius is 0.9992782 estimated iterations to convergence 294 setup time was (sec) 2.380000 now iterating at: 14:34:11 rms-change max change #iterations 11.01959 405.9428 at 10iterations 6.485645 141.0563 at 20iterations 3.781914 81.89245 at 30iterations 2.209273 44.51527 at 40iterations 1.283315 21.82446 at 50iterations 0.7458137 14.00768 at 60iterations 0.4337422 8.013119 at 70iterations 0.2515535 4.443416 at 80iterations 0.1459381 2.636437 at 90iterations 8.4473617E-02 1.722797 at 100iterations 4.8877679E-02 0.7567120 at 110iterations 2.8356854E-02 0.4666023 at 120iterations 1.6411657E-02 0.2752994 at 130iterations 9.5143914E-03 0.1621618 at 140iterations 5.5011422E-03 9.1596603E-02 at 150iterations 3.1930981E-03 5.3874969E-02 at 160iterations 1.8454044E-03 3.1737685E-02 at 170iterations 1.0693059E-03 1.7692566E-02 at 180iterations finished qdiffx linear iterations at : 14:34:26 total time elapsed so far: 16.94000 # loops : 180 mean,max change (kT/e) : 1.0693059E-03 1.7692566E-02 energy calculations done at 16.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.12000 DelPhi exited at 14:34:26 17.120u 0.344s 0:17.75 98.3% 0+0k 0+0io 0pf+0w