Mon Oct 10 19:37:25 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 19:37:26 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 = 2877 !!! WARNING: GLM 115 has a net charge of -0.0940 !!! WARNING: LEU 314 has a net charge of -0.0260 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: 0.6130849 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): -33.97900 20.94600 ymin,ymax (A): 40.68100 89.58300 zmin,zma (A): 0.2960000 58.36300 x,y,z range (A): 54.92500 48.90200 58.06700 scale (grids/A): 0.6130849 object centre (A): -6.516500 65.13200 29.32950 number of atom coordinates read : 2877 total number of charged atoms : 2730 net assigned charge : 0.3800132 assigned positive charge : 430.3203 centred at (gu) : 92.00350 89.97560 89.11193 assigned negative charge : -429.9409 centred at (gu) : 91.92300 90.05944 89.10771 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7119 nv = 96 ne = 84 npr = 57437 no. pairs analyzed = 57437 no. exposed pairs = 4118 no. arc points = 28128 no. surface atoms = 1358 nbur = 1519 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 3530 m= 0 mr = 33 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2637 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8810 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3772880E-10 3.2541353E-10 midg,1,midg; midg,igrid,midg 5.1387876E-09 -4.8933013E-09 1,midg,midg; igrid,midg,midg -3.0068625E-09 7.7761131E-09 gauss-seidel spectral radius is 0.9862545 estimated iterations to convergence 70 setup time was (sec) 0.6400000 now iterating at: 19:37:26 rms-change max change #iterations 0.1229512 18.43189 at 10iterations 1.1042534E-02 1.749993 at 20iterations 1.0413748E-03 0.1348143 at 30iterations 1.2007728E-04 2.0102501E-02 at 40iterations 2.3061855E-05 4.6291351E-03 at 50iterations finished qdiffx linear iterations at : 19:37:30 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 2.3061855E-05 4.6291351E-03 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 19:37:30 4.095u 0.259s 0:04.72 91.9% 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 19:37:30 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 = 2877 !!! WARNING: GLM 115 has a net charge of -0.0940 !!! WARNING: LEU 314 has a net charge of -0.0260 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: 1.839255 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): -33.97900 20.94600 ymin,ymax (A): 40.68100 89.58300 zmin,zma (A): 0.2960000 58.36300 x,y,z range (A): 54.92500 48.90200 58.06700 scale (grids/A): 1.839255 object centre (A): -6.516500 65.13200 29.32950 number of atom coordinates read : 2877 total number of charged atoms : 2730 net assigned charge : 0.3800132 assigned positive charge : 430.3203 centred at (gu) : 96.00967 89.92615 87.33504 assigned negative charge : -429.9409 centred at (gu) : 95.76868 90.17779 87.32255 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 76342 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28128 grid for indexing accessible points = 1.400000 m= 25866 mr = 49909 m= 3987 mr = 17684 m= 229 mr = 2203 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 296 time to turn everything in is 0.7000000 number of dielectric boundary points 36577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 21365 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) : 0.6130849 object centre at (A) : -6.516500 65.13200 29.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2690633E-02 -5.4484870E-02 midg,1,midg; midg,igrid,midg 6.1802454E-03 -1.7252561E-03 1,midg,midg; igrid,midg,midg -2.1018574E-02 1.2050771E-02 gauss-seidel spectral radius is 0.9985749 estimated iterations to convergence 210 setup time was (sec) 0.9900000 now iterating at: 19:37:32 rms-change max change #iterations 4.220179 189.7156 at 10iterations 1.934479 65.87788 at 20iterations 0.8875301 28.42540 at 30iterations 0.4086059 13.12476 at 40iterations 0.1878230 6.065444 at 50iterations 8.6451061E-02 2.713408 at 60iterations 3.9683796E-02 1.405355 at 70iterations 1.8257098E-02 0.6090393 at 80iterations 8.3944965E-03 0.2694468 at 90iterations 3.8780905E-03 0.1316203 at 100iterations 1.7901453E-03 5.8976650E-02 at 110iterations 8.2363083E-04 2.6523590E-02 at 120iterations finished qdiffx linear iterations at : 19:37:40 total time elapsed so far: 9.320000 # loops : 120 mean,max change (kT/e) : 8.2363083E-04 2.6523590E-02 energy calculations done at 9.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.500000 DelPhi exited at 19:37:40 9.506u 0.297s 0:10.17 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 Mon Oct 10 2011 at 19:37:41 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 = 2877 !!! WARNING: GLM 115 has a net charge of -0.0940 !!! WARNING: LEU 314 has a net charge of -0.0260 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: 2.758882 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): -33.97900 20.94600 ymin,ymax (A): 40.68100 89.58300 zmin,zma (A): 0.2960000 58.36300 x,y,z range (A): 54.92500 48.90200 58.06700 scale (grids/A): 2.758882 object centre (A): -6.516500 65.13200 29.32950 number of atom coordinates read : 2877 total number of charged atoms : 2730 net assigned charge : 0.3800132 assigned positive charge : 430.3203 centred at (gu) : 99.01433 89.88898 86.00237 assigned negative charge : -429.9409 centred at (gu) : 98.65291 90.26659 85.98363 start vw surface at 0.1700000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 176766 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28128 grid for indexing accessible points = 1.400000 m= 84060 mr = 122703 m= 29508 mr = 64947 m= 6813 mr = 22515 m= 920 mr = 4778 m= 37 mr = 482 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 867 time to turn everything in is 1.770000 number of dielectric boundary points 82678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 21833 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) : 1.839255 object centre at (A) : -6.516500 65.13200 29.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4881128 -0.9455155 midg,1,midg; midg,igrid,midg 5.6383707E-02 -2.9143587E-02 1,midg,midg; igrid,midg,midg -0.1419613 0.2020669 gauss-seidel spectral radius is 0.9992602 estimated iterations to convergence 290 setup time was (sec) 2.100000 now iterating at: 19:37:43 rms-change max change #iterations 10.34196 345.1800 at 10iterations 6.161813 158.4336 at 20iterations 3.637038 77.66260 at 30iterations 2.128750 45.99962 at 40iterations 1.241880 25.49518 at 50iterations 0.7230373 15.34471 at 60iterations 0.4189139 8.248250 at 70iterations 0.2425530 4.484804 at 80iterations 0.1406159 2.765060 at 90iterations 8.0915309E-02 1.502165 at 100iterations 4.6755202E-02 0.9597788 at 110iterations 2.6948884E-02 0.5099435 at 120iterations 1.5522603E-02 0.3022447 at 130iterations 8.9479694E-03 0.1642805 at 140iterations 5.1458846E-03 9.2893600E-02 at 150iterations 2.9638463E-03 5.7051659E-02 at 160iterations 1.7048018E-03 3.0536652E-02 at 170iterations 9.8130340E-04 1.8826485E-02 at 180iterations finished qdiffx linear iterations at : 19:37:57 total time elapsed so far: 15.96000 # loops : 180 mean,max change (kT/e) : 9.8130340E-04 1.8826485E-02 energy calculations done at 15.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.14000 DelPhi exited at 19:37:58 16.142u 0.291s 0:16.99 96.7% 0+0k 0+0io 0pf+0w