Sun Oct 9 09:40:27 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 09:40:27 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3142 !!! WARNING: TYR 304 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.4942659 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): -38.37900 16.57500 ymin,ymax (A): 3.324000 52.65700 zmin,zma (A): -3.125000 68.90100 x,y,z range (A): 54.95400 49.33300 72.02600 scale (grids/A): 0.4942659 object centre (A): -10.90200 27.99050 32.88800 number of atom coordinates read : 3142 total number of charged atoms : 2991 net assigned charge : 3.228023 assigned positive charge : 467.0310 centred at (gu) : 91.32771 89.79744 89.09875 assigned negative charge : -463.8041 centred at (gu) : 91.35716 89.81697 89.05473 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5022 nv = 96 ne = 84 npr = 60406 no. pairs analyzed = 60406 no. exposed pairs = 4459 no. arc points = 31703 no. surface atoms = 1477 nbur = 1665 mkacc time = 0.1100000 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 = 1.708000 m= 192 mr = 2322 m= 0 mr = 6 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2971 ## 454 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 6700 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8201178E-11 4.5438826E-11 midg,1,midg; midg,igrid,midg 4.0261378E-11 5.9424410E-12 1,midg,midg; igrid,midg,midg 3.2340013E-11 -3.2688821E-12 gauss-seidel spectral radius is 0.9789737 estimated iterations to convergence 57 setup time was (sec) 0.4100000 now iterating at: 09:40:27 rms-change max change #iterations 4.5652356E-02 10.70117 at 10iterations 2.2809685E-03 0.5233984 at 20iterations 1.2109370E-04 1.9897461E-02 at 30iterations 9.0366866E-06 2.1953583E-03 at 40iterations 1.4772081E-06 3.7288666E-04 at 50iterations finished qdiffx linear iterations at : 09:40:30 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.4772081E-06 3.7288666E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 09:40:31 3.468u 0.168s 0:03.92 92.3% 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 09:40:31 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3142 !!! WARNING: TYR 304 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.482798 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): -38.37900 16.57500 ymin,ymax (A): 3.324000 52.65700 zmin,zma (A): -3.125000 68.90100 x,y,z range (A): 54.95400 49.33300 72.02600 scale (grids/A): 1.482798 object centre (A): -10.90200 27.99050 32.88800 number of atom coordinates read : 3142 total number of charged atoms : 2991 net assigned charge : 3.228023 assigned positive charge : 467.0310 centred at (gu) : 93.98209 89.39143 87.29552 assigned negative charge : -463.8041 centred at (gu) : 94.07101 89.45042 87.16417 start vw surface at 0.1100000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 55818 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31703 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 15963 mr = 35316 m= 1353 mr = 10218 m= 26 mr = 487 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 228 time to turn everything in is 0.3100000 number of dielectric boundary points 27139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 458 ## 15 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 22272 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) : 0.4942659 object centre at (A) : -10.90200 27.99050 32.88800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5334494E-03 -1.1049828E-02 midg,1,midg; midg,igrid,midg 5.0629172E-03 2.9734700E-04 1,midg,midg; igrid,midg,midg 2.9376263E-03 -1.4419629E-03 gauss-seidel spectral radius is 0.9978110 estimated iterations to convergence 170 setup time was (sec) 0.5200000 now iterating at: 09:40:31 rms-change max change #iterations 2.727118 134.7947 at 10iterations 1.033864 45.33185 at 20iterations 0.3968703 18.23691 at 30iterations 0.1510001 6.401850 at 40iterations 5.7829130E-02 2.412620 at 50iterations 2.2083713E-02 0.8518486 at 60iterations 8.4263850E-03 0.3345947 at 70iterations 3.2437625E-03 0.1402798 at 80iterations 1.2469165E-03 5.1628113E-02 at 90iterations 4.8460212E-04 2.1256447E-02 at 100iterations 1.9114063E-04 8.7270737E-03 at 110iterations 7.9238416E-05 3.3798218E-03 at 120iterations finished qdiffx linear iterations at : 09:40:38 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 7.9238416E-05 3.3798218E-03 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 09:40:39 7.664u 0.188s 0:08.17 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 Sun Oct 9 2011 at 09:40:39 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3142 !!! WARNING: TYR 304 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.224197 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): -38.37900 16.57500 ymin,ymax (A): 3.324000 52.65700 zmin,zma (A): -3.125000 68.90100 x,y,z range (A): 54.95400 49.33300 72.02600 scale (grids/A): 2.224197 object centre (A): -10.90200 27.99050 32.88800 number of atom coordinates read : 3142 total number of charged atoms : 2991 net assigned charge : 3.228023 assigned positive charge : 467.0310 centred at (gu) : 95.97278 89.08696 85.94304 assigned negative charge : -463.8041 centred at (gu) : 96.10640 89.17553 85.74617 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 130190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31703 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 55933 mr = 87706 m= 14250 mr = 42210 m= 1673 mr = 9936 m= 57 mr = 966 m= 0 mr = 12 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 877 time to turn everything in is 0.7000000 number of dielectric boundary points 61273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 23846 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) : 1.482798 object centre at (A) : -10.90200 27.99050 32.88800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4262893E-02 -0.1933679 midg,1,midg; midg,igrid,midg 8.8577367E-02 3.9333128E-03 1,midg,midg; igrid,midg,midg 6.7062043E-02 -1.9109320E-02 gauss-seidel spectral radius is 0.9990247 estimated iterations to convergence 253 setup time was (sec) 0.9300000 now iterating at: 09:40:40 rms-change max change #iterations 7.680122 269.0339 at 10iterations 4.203561 122.1838 at 20iterations 2.274104 60.96877 at 30iterations 1.220430 37.45738 at 40iterations 0.6521628 16.32737 at 50iterations 0.3490062 9.462093 at 60iterations 0.1853350 4.645143 at 70iterations 9.8528780E-02 2.720543 at 80iterations 5.2282445E-02 1.316624 at 90iterations 2.7660742E-02 0.6555367 at 100iterations 1.4669538E-02 0.3454580 at 110iterations 7.7616638E-03 0.1718674 at 120iterations 4.1077109E-03 0.1003761 at 130iterations 2.1725439E-03 6.2345505E-02 at 140iterations 1.1514828E-03 2.6863098E-02 at 150iterations 6.0870632E-04 1.4171600E-02 at 160iterations 3.2089822E-04 8.0871582E-03 at 170iterations 1.7055203E-04 4.1990280E-03 at 180iterations finished qdiffx linear iterations at : 09:40:51 total time elapsed so far: 12.01000 # loops : 180 mean,max change (kT/e) : 1.7055203E-04 4.1990280E-03 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.14000 DelPhi exited at 09:40:52 12.142u 0.188s 0:12.60 97.7% 0+0k 0+0io 0pf+0w