Mon Oct 10 13:59:17 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 13:59:17 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2590 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 504 has a net charge of 1.4000 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: 0.6243861 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): -31.30600 17.69700 ymin,ymax (A): -23.78700 22.76100 zmin,zma (A): -12.46700 44.54900 x,y,z range (A): 49.00300 46.54800 57.01600 scale (grids/A): 0.6243861 object centre (A): -6.804500 -0.5129995 16.04100 number of atom coordinates read : 2590 total number of charged atoms : 2464 net assigned charge : 3.906008 assigned positive charge : 394.1361 centred at (gu) : 88.36172 89.20404 89.77586 assigned negative charge : -390.2305 centred at (gu) : 88.25880 89.26332 89.66996 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6516 nv = 96 ne = 84 npr = 54032 no. pairs analyzed = 54032 no. exposed pairs = 2969 no. arc points = 21467 no. surface atoms = 999 nbur = 1591 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 321 mr = 3598 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 116 time to turn everything in is 0.3500000 number of dielectric boundary points 3194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2147 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 8175 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6187791E-09 1.1064314E-08 midg,1,midg; midg,igrid,midg 9.7176347E-09 -6.3815697E-10 1,midg,midg; igrid,midg,midg -6.1131384E-09 7.9881346E-09 gauss-seidel spectral radius is 0.9867100 estimated iterations to convergence 71 setup time was (sec) 0.8500000 now iterating at: 13:59:19 rms-change max change #iterations 0.1345436 24.02033 at 10iterations 1.2389340E-02 1.785991 at 20iterations 1.1796404E-03 0.1815605 at 30iterations 1.0944626E-04 1.8413544E-02 at 40iterations 1.0336704E-05 1.5029907E-03 at 50iterations finished qdiffx linear iterations at : 13:59:24 total time elapsed so far: 6.140000 # loops : 50 mean,max change (kT/e) : 1.0336704E-05 1.5029907E-03 energy calculations done at 6.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.320000 DelPhi exited at 13:59:24 6.321u 0.638s 0:07.39 94.0% 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 13:59:25 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2590 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 504 has a net charge of 1.4000 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: 1.873158 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): -31.30600 17.69700 ymin,ymax (A): -23.78700 22.76100 zmin,zma (A): -12.46700 44.54900 x,y,z range (A): 49.00300 46.54800 57.01600 scale (grids/A): 1.873158 object centre (A): -6.804500 -0.5129995 16.04100 number of atom coordinates read : 2590 total number of charged atoms : 2464 net assigned charge : 3.906008 assigned positive charge : 394.1361 centred at (gu) : 85.08466 87.61169 89.32713 assigned negative charge : -390.2305 centred at (gu) : 84.77618 87.78967 89.00967 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71612 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21467 grid for indexing accessible points = 1.400000 m= 24060 mr = 50050 m= 3276 mr = 17627 m= 125 mr = 1962 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 5261 time to turn everything in is 0.5900000 number of dielectric boundary points 29390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 19372 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) : 0.6243861 object centre at (A) : -6.804500 -0.5129995 16.04100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7381461E-02 1.4981280E-02 midg,1,midg; midg,igrid,midg 1.5588699E-02 4.4653728E-03 1,midg,midg; igrid,midg,midg -1.7818126E-03 3.8978584E-02 gauss-seidel spectral radius is 0.9985857 estimated iterations to convergence 211 setup time was (sec) 0.9500000 now iterating at: 13:59:26 rms-change max change #iterations 4.087058 182.6055 at 10iterations 1.887842 64.15500 at 20iterations 0.8692046 31.99487 at 30iterations 0.4014958 13.86954 at 40iterations 0.1863736 5.538265 at 50iterations 8.5968547E-02 2.887959 at 60iterations 3.9864477E-02 1.315941 at 70iterations 1.8422140E-02 0.6241684 at 80iterations 8.5095270E-03 0.2891865 at 90iterations 3.9297529E-03 0.1234970 at 100iterations 1.8143107E-03 5.6461334E-02 at 110iterations 8.3925732E-04 2.6191711E-02 at 120iterations finished qdiffx linear iterations at : 13:59:43 total time elapsed so far: 18.42000 # loops : 120 mean,max change (kT/e) : 8.3925732E-04 2.6191711E-02 energy calculations done at 18.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.60000 DelPhi exited at 13:59:45 18.607u 0.554s 0:20.21 94.7% 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 13:59:47 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2590 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 504 has a net charge of 1.4000 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: 2.809738 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): -31.30600 17.69700 ymin,ymax (A): -23.78700 22.76100 zmin,zma (A): -12.46700 44.54900 x,y,z range (A): 49.00300 46.54800 57.01600 scale (grids/A): 2.809738 object centre (A): -6.804500 -0.5129995 16.04100 number of atom coordinates read : 2590 total number of charged atoms : 2464 net assigned charge : 3.906008 assigned positive charge : 394.1361 centred at (gu) : 82.62691 86.41743 88.99074 assigned negative charge : -390.2305 centred at (gu) : 82.16419 86.68441 88.51446 start vw surface at 0.1200000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 165946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21467 grid for indexing accessible points = 1.400000 m= 80785 mr = 121296 m= 26322 mr = 66282 m= 5613 mr = 20967 m= 629 mr = 4130 m= 22 mr = 383 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 17720 time to turn everything in is 1.760000 number of dielectric boundary points 66249 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 19708 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) : 1.873158 object centre at (A) : -6.804500 -0.5129995 16.04100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1013281 0.1692359 midg,1,midg; midg,igrid,midg 0.1787481 2.7329434E-02 1,midg,midg; igrid,midg,midg -9.5511097E-03 0.5118893 gauss-seidel spectral radius is 0.9992391 estimated iterations to convergence 286 setup time was (sec) 2.430000 now iterating at: 13:59:50 rms-change max change #iterations 9.582725 292.0209 at 10iterations 5.513878 160.1731 at 20iterations 3.151879 61.96924 at 30iterations 1.800739 35.38806 at 40iterations 1.027827 24.26266 at 50iterations 0.5849926 12.43732 at 60iterations 0.3345173 6.387496 at 70iterations 0.1906323 3.646123 at 80iterations 0.1086910 2.667290 at 90iterations 6.1921939E-02 1.225716 at 100iterations 3.5248458E-02 0.7115726 at 110iterations 2.0113220E-02 0.3820553 at 120iterations 1.1452855E-02 0.2323532 at 130iterations 6.5380638E-03 0.1266336 at 140iterations 3.7209471E-03 6.5776825E-02 at 150iterations 2.1255855E-03 4.0332794E-02 at 160iterations 1.2120777E-03 2.2017419E-02 at 170iterations 6.9150160E-04 1.3328552E-02 at 180iterations finished qdiffx linear iterations at : 14:00:16 total time elapsed so far: 28.13000 # loops : 180 mean,max change (kT/e) : 6.9150160E-04 1.3328552E-02 energy calculations done at 28.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 28.33000 DelPhi exited at 14:00:17 28.333u 0.935s 0:30.01 97.5% 0+0k 0+0io 0pf+0w