Sun Oct 9 14:04:58 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 Sun Oct 9 2011 at 14:04:58 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2373 !!! WARNING: GLM 182 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6890144 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): 21.36800 70.38500 ymin,ymax (A): -1.748000 49.92000 zmin,zma (A): -5.585000 37.30200 x,y,z range (A): 49.01700 51.66800 42.88700 scale (grids/A): 0.6890144 object centre (A): 45.87650 24.08600 15.85850 number of atom coordinates read : 2373 total number of charged atoms : 2227 net assigned charge : 3.406023 assigned positive charge : 364.5862 centred at (gu) : 90.33802 89.16905 89.02561 assigned negative charge : -361.1806 centred at (gu) : 90.36670 89.03184 88.93547 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7608 nv = 96 ne = 84 npr = 47734 no. pairs analyzed = 47734 no. exposed pairs = 2859 no. arc points = 20491 no. surface atoms = 965 nbur = 1408 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 429 mr = 4272 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2700000 number of dielectric boundary points 3714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1908 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8644 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8329988E-08 4.3458360E-08 midg,1,midg; midg,igrid,midg -3.9173276E-08 5.9265268E-08 1,midg,midg; igrid,midg,midg 2.8081224E-08 9.0566843E-09 gauss-seidel spectral radius is 0.9890556 estimated iterations to convergence 78 setup time was (sec) 0.4900000 now iterating at: 14:04:59 rms-change max change #iterations 0.1940982 27.46012 at 10iterations 2.2761747E-02 3.247974 at 20iterations 2.7514093E-03 0.3334808 at 30iterations 3.6595869E-04 4.7298431E-02 at 40iterations 6.3617117E-05 9.7885132E-03 at 50iterations finished qdiffx linear iterations at : 14:05:01 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 6.3617117E-05 9.7885132E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 14:05:02 3.072u 0.129s 0:03.63 87.8% 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 Sun Oct 9 2011 at 14:05:02 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2373 !!! WARNING: GLM 182 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.067043 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): 21.36800 70.38500 ymin,ymax (A): -1.748000 49.92000 zmin,zma (A): -5.585000 37.30200 x,y,z range (A): 49.01700 51.66800 42.88700 scale (grids/A): 2.067043 object centre (A): 45.87650 24.08600 15.85850 number of atom coordinates read : 2373 total number of charged atoms : 2227 net assigned charge : 3.406023 assigned positive charge : 364.5862 centred at (gu) : 91.01359 87.50674 87.07682 assigned negative charge : -361.1806 centred at (gu) : 91.09973 87.09536 86.80624 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 81471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20491 grid for indexing accessible points = 1.400000 m= 30370 mr = 57166 m= 5120 mr = 22765 m= 483 mr = 3321 m= 13 mr = 251 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1556 time to turn everything in is 0.5600000 number of dielectric boundary points 33954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17678 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) : 0.6890144 object centre at (A) : 45.87650 24.08600 15.85850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1011609E-03 4.7236599E-02 midg,1,midg; midg,igrid,midg -2.7165227E-02 1.4530627E-02 1,midg,midg; igrid,midg,midg 3.7543755E-02 -1.0945046E-02 gauss-seidel spectral radius is 0.9988095 estimated iterations to convergence 229 setup time was (sec) 0.8300000 now iterating at: 14:05:03 rms-change max change #iterations 4.817906 224.4928 at 10iterations 2.362820 82.05128 at 20iterations 1.165217 40.31988 at 30iterations 0.5751645 15.96563 at 40iterations 0.2838390 9.044958 at 50iterations 0.1395647 4.251251 at 60iterations 6.8867415E-02 2.071320 at 70iterations 3.3990141E-02 0.9778748 at 80iterations 1.6838318E-02 0.4884491 at 90iterations 8.2964506E-03 0.2538013 at 100iterations 4.1211909E-03 0.1311646 at 110iterations 2.0510361E-03 6.1988831E-02 at 120iterations finished qdiffx linear iterations at : 14:05:09 total time elapsed so far: 6.820000 # loops : 120 mean,max change (kT/e) : 2.0510361E-03 6.1988831E-02 energy calculations done at 6.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 14:05:09 7.005u 0.135s 0:07.41 96.2% 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 Sun Oct 9 2011 at 14:05:09 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2373 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 3.100565 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): 21.36800 70.38500 ymin,ymax (A): -1.748000 49.92000 zmin,zma (A): -5.585000 37.30200 x,y,z range (A): 49.01700 51.66800 42.88700 scale (grids/A): 3.100565 object centre (A): 45.87650 24.08600 15.85850 number of atom coordinates read : 2373 total number of charged atoms : 2227 net assigned charge : 3.406023 assigned positive charge : 364.5862 centred at (gu) : 91.52032 86.26002 85.61494 assigned negative charge : -361.1806 centred at (gu) : 91.64952 85.64288 85.20926 start vw surface at 0.1600000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 187820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20491 grid for indexing accessible points = 1.400000 m= 97640 mr = 137925 m= 36544 mr = 80758 m= 9527 mr = 29662 m= 1858 mr = 7251 m= 235 mr = 1370 m= 11 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 5055 time to turn everything in is 1.800000 number of dielectric boundary points 76492 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 17816 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) : 2.067043 object centre at (A) : 45.87650 24.08600 15.85850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3440489E-02 0.4460438 midg,1,midg; midg,igrid,midg -0.2642615 0.3729896 1,midg,midg; igrid,midg,midg 0.3954031 -0.3935219 gauss-seidel spectral radius is 0.9992918 estimated iterations to convergence 296 setup time was (sec) 2.100000 now iterating at: 14:05:12 rms-change max change #iterations 10.86786 456.3549 at 10iterations 6.396124 148.1555 at 20iterations 3.758050 68.03455 at 30iterations 2.208973 46.47051 at 40iterations 1.296896 25.39652 at 50iterations 0.7585459 13.27215 at 60iterations 0.4440578 9.404325 at 70iterations 0.2594953 4.410133 at 80iterations 0.1518063 2.667767 at 90iterations 8.8724591E-02 1.748573 at 100iterations 5.1769242E-02 0.8633122 at 110iterations 3.0148396E-02 0.5176220 at 120iterations 1.7661018E-02 0.2795277 at 130iterations 1.0311687E-02 0.1855965 at 140iterations 6.0586124E-03 0.1103897 at 150iterations 3.5548743E-03 6.0808182E-02 at 160iterations 2.1051094E-03 3.6499977E-02 at 170iterations 1.2565401E-03 2.3784637E-02 at 180iterations finished qdiffx linear iterations at : 14:05:21 total time elapsed so far: 11.53000 # loops : 180 mean,max change (kT/e) : 1.2565401E-03 2.3784637E-02 energy calculations done at 11.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.74000 DelPhi exited at 14:05:22 11.743u 0.175s 0:12.22 97.4% 0+0k 0+0io 0pf+0w