Tue Oct 11 03:19:52 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+sph.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 = amb.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 03:19:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3396 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SER 496 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5660408 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): -10.97800 43.93200 ymin,ymax (A): 14.35300 75.68200 zmin,zma (A): 39.71800 102.6110 x,y,z range (A): 54.91000 61.32900 62.89300 scale (grids/A): 0.5660408 object centre (A): 16.47700 45.01750 71.16451 number of atom coordinates read : 3396 total number of charged atoms : 3257 net assigned charge : -7.043968 assigned positive charge : 512.3784 centred at (gu) : 88.27262 87.84892 88.14504 assigned negative charge : -519.4237 centred at (gu) : 88.30179 87.82640 88.13427 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7024 nv = 96 ne = 84 npr = 69281 no. pairs analyzed = 69281 no. exposed pairs = 4326 no. arc points = 30588 no. surface atoms = 1453 nbur = 1943 mkacc time = 0.1600000 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 = 1.512000 m= 330 mr = 3603 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3105 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9084 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6904509E-09 -4.9273807E-10 midg,1,midg; midg,igrid,midg -2.1312507E-09 -3.5108416E-10 1,midg,midg; igrid,midg,midg -6.7715339E-10 -9.2375385E-10 gauss-seidel spectral radius is 0.9839299 estimated iterations to convergence 65 setup time was (sec) 0.6200000 now iterating at: 03:19:53 rms-change max change #iterations 9.6609004E-02 13.81600 at 10iterations 7.0963362E-03 1.105096 at 20iterations 6.1338261E-04 9.7488403E-02 at 30iterations 1.0575561E-04 1.6648769E-02 at 40iterations 3.2252661E-05 6.0086250E-03 at 50iterations finished qdiffx linear iterations at : 03:19:55 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 3.2252661E-05 6.0086250E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 03:19:56 3.391u 0.150s 0:03.99 88.7% 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 03:19:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3396 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SER 496 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.698122 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): -10.97800 43.93200 ymin,ymax (A): 14.35300 75.68200 zmin,zma (A): 39.71800 102.6110 x,y,z range (A): 54.91000 61.32900 62.89300 scale (grids/A): 1.698122 object centre (A): 16.47700 45.01750 71.16451 number of atom coordinates read : 3396 total number of charged atoms : 3257 net assigned charge : -7.043968 assigned positive charge : 512.3784 centred at (gu) : 84.81687 83.54555 84.43397 assigned negative charge : -519.4237 centred at (gu) : 84.90495 83.47886 84.40236 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 75968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30588 grid for indexing accessible points = 1.400000 m= 26191 mr = 50910 m= 3404 mr = 18685 m= 115 mr = 1770 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 541 time to turn everything in is 0.6100000 number of dielectric boundary points 34296 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 299 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 25118 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) : 0.5660408 object centre at (A) : 16.47700 45.01750 71.16451 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7316202E-02 3.4132846E-02 midg,1,midg; midg,igrid,midg -6.7905406E-03 4.0820483E-03 1,midg,midg; igrid,midg,midg -2.1204751E-03 4.7372689E-04 gauss-seidel spectral radius is 0.9983626 estimated iterations to convergence 196 setup time was (sec) 0.8800000 now iterating at: 03:19:57 rms-change max change #iterations 3.937776 190.3916 at 10iterations 1.701372 62.19006 at 20iterations 0.7406974 24.94367 at 30iterations 0.3226310 10.43464 at 40iterations 0.1406856 4.487375 at 50iterations 6.1096650E-02 2.073090 at 60iterations 2.6718559E-02 0.9159784 at 70iterations 1.1666493E-02 0.4495077 at 80iterations 5.0894865E-03 0.1758919 at 90iterations 2.2468194E-03 7.9177856E-02 at 100iterations 9.9917292E-04 3.0946732E-02 at 110iterations 4.5444339E-04 1.5982628E-02 at 120iterations finished qdiffx linear iterations at : 03:20:03 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 4.5444339E-04 1.5982628E-02 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 03:20:04 7.462u 0.163s 0:08.13 93.7% 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 03:20:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3396 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SER 496 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.547184 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): -10.97800 43.93200 ymin,ymax (A): 14.35300 75.68200 zmin,zma (A): 39.71800 102.6110 x,y,z range (A): 54.91000 61.32900 62.89300 scale (grids/A): 2.547184 object centre (A): 16.47700 45.01750 71.16451 number of atom coordinates read : 3396 total number of charged atoms : 3257 net assigned charge : -7.043968 assigned positive charge : 512.3784 centred at (gu) : 82.22522 80.31826 81.65079 assigned negative charge : -519.4237 centred at (gu) : 82.35726 80.21815 81.60342 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 175882 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30588 grid for indexing accessible points = 1.400000 m= 86230 mr = 124245 m= 29155 mr = 68985 m= 5495 mr = 22812 m= 525 mr = 3664 m= 15 mr = 265 m= 0 mr = 2 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 1611 time to turn everything in is 1.410000 number of dielectric boundary points 77329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 26037 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) : 1.698122 object centre at (A) : 16.47700 45.01750 71.16451 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3508613 0.8827271 midg,1,midg; midg,igrid,midg -5.1913611E-03 0.2476778 1,midg,midg; igrid,midg,midg 2.4402016E-03 -1.8979421E-02 gauss-seidel spectral radius is 0.9992033 estimated iterations to convergence 280 setup time was (sec) 1.710000 now iterating at: 03:20:06 rms-change max change #iterations 9.934937 292.8981 at 10iterations 5.719920 170.0383 at 20iterations 3.272120 80.52061 at 30iterations 1.866294 42.27234 at 40iterations 1.059058 22.53906 at 50iterations 0.6000142 14.12468 at 60iterations 0.3393874 6.804869 at 70iterations 0.1918428 3.478219 at 80iterations 0.1083162 2.230217 at 90iterations 6.0935833E-02 1.147783 at 100iterations 3.4408182E-02 0.6954193 at 110iterations 1.9380029E-02 0.3548179 at 120iterations 1.0921439E-02 0.2081714 at 130iterations 6.1569097E-03 0.1194696 at 140iterations 3.4695133E-03 6.7405820E-02 at 150iterations 1.9546435E-03 4.1048050E-02 at 160iterations 1.1071289E-03 2.2337914E-02 at 170iterations 6.3077436E-04 1.1064529E-02 at 180iterations finished qdiffx linear iterations at : 03:20:16 total time elapsed so far: 12.07000 # loops : 180 mean,max change (kT/e) : 6.3077436E-04 1.1064529E-02 energy calculations done at 12.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 03:20:17 12.257u 0.192s 0:12.92 96.2% 0+0k 0+0io 0pf+0w