Tue Oct 11 08:34:19 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 Tue Oct 11 2011 at 08:34:19 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7066016 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): -20.16900 26.45500 ymin,ymax (A): -28.44000 11.14600 zmin,zma (A): -13.62800 36.75400 x,y,z range (A): 46.62400 39.58600 50.38200 scale (grids/A): 0.7066016 object centre (A): 3.143001 -8.647000 11.56300 number of atom coordinates read : 2073 total number of charged atoms : 1939 net assigned charge : 5.931010 assigned positive charge : 315.3441 centred at (gu) : 89.49062 90.62630 89.35849 assigned negative charge : -309.4131 centred at (gu) : 89.34900 90.59332 89.29868 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6993 nv = 96 ne = 84 npr = 42036 no. pairs analyzed = 42036 no. exposed pairs = 2451 no. arc points = 16677 no. surface atoms = 837 nbur = 1236 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 453 mr = 4096 m= 7 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1627 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7796 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3043764E-08 6.9117846E-08 midg,1,midg; midg,igrid,midg 3.0028641E-08 7.3727257E-08 1,midg,midg; igrid,midg,midg -2.1944027E-08 1.0572395E-07 gauss-seidel spectral radius is 0.9895566 estimated iterations to convergence 80 setup time was (sec) 0.3400000 now iterating at: 08:34:20 rms-change max change #iterations 0.1994356 25.95787 at 10iterations 2.5185812E-02 3.699782 at 20iterations 3.2052991E-03 0.4963927 at 30iterations 4.6860715E-04 6.5686226E-02 at 40iterations 9.2242335E-05 1.4099121E-02 at 50iterations finished qdiffx linear iterations at : 08:34:23 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 9.2242335E-05 1.4099121E-02 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 08:34:23 3.296u 0.171s 0:03.99 86.7% 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 Tue Oct 11 2011 at 08:34:23 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.119805 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): -20.16900 26.45500 ymin,ymax (A): -28.44000 11.14600 zmin,zma (A): -13.62800 36.75400 x,y,z range (A): 46.62400 39.58600 50.38200 scale (grids/A): 2.119805 object centre (A): 3.143001 -8.647000 11.56300 number of atom coordinates read : 2073 total number of charged atoms : 1939 net assigned charge : 5.931010 assigned positive charge : 315.3441 centred at (gu) : 88.47165 91.87905 88.07543 assigned negative charge : -309.4131 centred at (gu) : 88.04699 91.78018 87.89611 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74487 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16677 grid for indexing accessible points = 1.400000 m= 29470 mr = 53576 m= 5461 mr = 22420 m= 481 mr = 3569 m= 9 mr = 236 m= 0 mr = 0 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 30107 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15408 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) : 0.7066016 object centre at (A) : 3.143001 -8.647000 11.56300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9572724E-02 4.1004609E-02 midg,1,midg; midg,igrid,midg 4.0551638E-03 3.4038752E-02 1,midg,midg; igrid,midg,midg 9.9873673E-03 3.0018942E-02 gauss-seidel spectral radius is 0.9988253 estimated iterations to convergence 231 setup time was (sec) 0.5900000 now iterating at: 08:34:24 rms-change max change #iterations 4.570483 199.6523 at 10iterations 2.258422 74.47928 at 20iterations 1.119557 38.32202 at 30iterations 0.5558228 18.72530 at 40iterations 0.2754255 8.140915 at 50iterations 0.1368546 4.396277 at 60iterations 6.8028629E-02 2.037280 at 70iterations 3.3902388E-02 1.129354 at 80iterations 1.6903274E-02 0.5332069 at 90iterations 8.4553743E-03 0.2858315 at 100iterations 4.2275907E-03 0.1251669 at 110iterations 2.1500438E-03 6.3491821E-02 at 120iterations finished qdiffx linear iterations at : 08:34:31 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 2.1500438E-03 6.3491821E-02 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 08:34:32 7.665u 0.181s 0:08.24 95.1% 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 Tue Oct 11 2011 at 08:34:32 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.179707 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): -20.16900 26.45500 ymin,ymax (A): -28.44000 11.14600 zmin,zma (A): -13.62800 36.75400 x,y,z range (A): 46.62400 39.58600 50.38200 scale (grids/A): 3.179707 object centre (A): 3.143001 -8.647000 11.56300 number of atom coordinates read : 2073 total number of charged atoms : 1939 net assigned charge : 5.931010 assigned positive charge : 315.3441 centred at (gu) : 87.70757 92.81857 87.11310 assigned negative charge : -309.4131 centred at (gu) : 87.07045 92.67026 86.84416 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 171932 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16677 grid for indexing accessible points = 1.400000 m= 92668 mr = 128877 m= 36781 mr = 77319 m= 10178 mr = 30128 m= 1921 mr = 7846 m= 197 mr = 1382 m= 5 mr = 113 m= 0 mr = 2 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.130000 number of dielectric boundary points 68015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 15512 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) : 2.119805 object centre at (A) : 3.143001 -8.647000 11.56300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8049811 0.3556103 midg,1,midg; midg,igrid,midg 9.8827034E-03 0.2762634 1,midg,midg; igrid,midg,midg 0.2321286 0.2650516 gauss-seidel spectral radius is 0.9992908 estimated iterations to convergence 296 setup time was (sec) 1.340000 now iterating at: 08:34:33 rms-change max change #iterations 10.26654 335.5351 at 10iterations 6.071935 159.3660 at 20iterations 3.570264 66.67298 at 30iterations 2.104166 43.76205 at 40iterations 1.233428 23.65882 at 50iterations 0.7230800 12.88176 at 60iterations 0.4242293 7.839249 at 70iterations 0.2476887 4.694355 at 80iterations 0.1451014 2.429943 at 90iterations 8.4959790E-02 1.538237 at 100iterations 4.9734574E-02 0.8517160 at 110iterations 2.9325468E-02 0.5031307 at 120iterations 1.7375236E-02 0.3329506 at 130iterations 1.0407956E-02 0.2024522 at 140iterations 6.4045722E-03 0.1145020 at 150iterations 4.0446129E-03 7.1075439E-02 at 160iterations 2.6928794E-03 5.6701660E-02 at 170iterations 1.8945195E-03 3.5339355E-02 at 180iterations finished qdiffx linear iterations at : 08:34:44 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 1.8945195E-03 3.5339355E-02 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 08:34:45 12.481u 0.213s 0:12.99 97.6% 0+0k 0+0io 0pf+0w