Mon Oct 10 14:08:31 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 14:08:31 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2728 !!! WARNING: MG3 365 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5065525 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): 22.16600 78.16600 ymin,ymax (A): -10.92100 59.35800 zmin,zma (A): 3.195000 54.98600 x,y,z range (A): 56.00000 70.27900 51.79100 scale (grids/A): 0.5065525 object centre (A): 50.16600 24.21850 29.09050 number of atom coordinates read : 2728 total number of charged atoms : 2593 net assigned charge : 2.400012 assigned positive charge : 399.3738 centred at (gu) : 89.79685 87.34689 90.04903 assigned negative charge : -396.9742 centred at (gu) : 89.73027 87.26063 89.97500 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 4517 nv = 96 ne = 84 npr = 54611 no. pairs analyzed = 54611 no. exposed pairs = 3537 no. arc points = 25608 no. surface atoms = 1195 nbur = 1533 mkacc time = 0.1300000 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 = 1.680000 m= 150 mr = 2132 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2584 ## 437 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 6033 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7394006E-11 1.2089292E-10 midg,1,midg; midg,igrid,midg -1.5329686E-10 6.6571214E-11 1,midg,midg; igrid,midg,midg -5.1913522E-11 1.0474658E-10 gauss-seidel spectral radius is 0.9799308 estimated iterations to convergence 58 setup time was (sec) 0.5900000 now iterating at: 14:08:32 rms-change max change #iterations 4.6918746E-02 8.914114 at 10iterations 2.6030368E-03 0.5416985 at 20iterations 1.3620108E-04 2.2418976E-02 at 30iterations 7.5436233E-06 1.5945435E-03 at 40iterations 4.4372339E-07 9.2506409E-05 at 50iterations finished qdiffx linear iterations at : 14:08:35 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 4.4372339E-07 9.2506409E-05 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 14:08:35 3.582u 0.185s 0:04.09 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 14:08:35 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2728 !!! WARNING: MG3 365 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.519657 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): 22.16600 78.16600 ymin,ymax (A): -10.92100 59.35800 zmin,zma (A): 3.195000 54.98600 x,y,z range (A): 56.00000 70.27900 51.79100 scale (grids/A): 1.519657 object centre (A): 50.16600 24.21850 29.09050 number of atom coordinates read : 2728 total number of charged atoms : 2593 net assigned charge : 2.400012 assigned positive charge : 399.3738 centred at (gu) : 89.39009 82.04001 90.14636 assigned negative charge : -396.9742 centred at (gu) : 89.19048 81.78143 89.92458 start vw surface at 0.1700000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 50945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25608 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 13607 mr = 32954 m= 1069 mr = 8548 m= 12 mr = 372 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 113 time to turn everything in is 0.4300000 number of dielectric boundary points 23759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 345 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 19457 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) : 0.5065525 object centre at (A) : 50.16600 24.21850 29.09050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1042231E-03 1.8012989E-03 midg,1,midg; midg,igrid,midg 5.4556816E-03 1.7399592E-02 1,midg,midg; igrid,midg,midg -7.8762854E-03 3.5156605E-03 gauss-seidel spectral radius is 0.9978531 estimated iterations to convergence 172 setup time was (sec) 0.7300000 now iterating at: 14:08:36 rms-change max change #iterations 2.681707 142.9898 at 10iterations 1.023775 53.81794 at 20iterations 0.3949813 16.41945 at 30iterations 0.1527219 6.649245 at 40iterations 5.8911461E-02 2.738267 at 50iterations 2.2670489E-02 0.9270716 at 60iterations 8.7493733E-03 0.4082527 at 70iterations 3.3755251E-03 0.1307489 at 80iterations 1.3031168E-03 5.4222107E-02 at 90iterations 5.0194672E-04 2.3731232E-02 at 100iterations 1.9485790E-04 1.0665894E-02 at 110iterations 7.4863703E-05 3.3817291E-03 at 120iterations finished qdiffx linear iterations at : 14:08:43 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 7.4863703E-05 3.3817291E-03 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 14:08:44 7.785u 0.252s 0:08.47 94.8% 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 14:08:44 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2728 !!! WARNING: MG3 365 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.279486 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): 22.16600 78.16600 ymin,ymax (A): -10.92100 59.35800 zmin,zma (A): 3.195000 54.98600 x,y,z range (A): 56.00000 70.27900 51.79100 scale (grids/A): 2.279486 object centre (A): 50.16600 24.21850 29.09050 number of atom coordinates read : 2728 total number of charged atoms : 2593 net assigned charge : 2.400012 assigned positive charge : 399.3738 centred at (gu) : 89.08492 78.05981 90.21935 assigned negative charge : -396.9742 centred at (gu) : 88.78567 77.67210 89.88669 start vw surface at 0.1600000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 118458 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25608 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 49385 mr = 81113 m= 11521 mr = 37466 m= 1411 mr = 7901 m= 65 mr = 720 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 411 time to turn everything in is 1.020000 number of dielectric boundary points 53629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 48 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 20687 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) : 1.519657 object centre at (A) : 50.16600 24.21850 29.09050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3277650E-02 2.0654047E-02 midg,1,midg; midg,igrid,midg 0.1067573 0.3664880 1,midg,midg; igrid,midg,midg -0.1796332 5.8753017E-02 gauss-seidel spectral radius is 0.9990118 estimated iterations to convergence 252 setup time was (sec) 1.350000 now iterating at: 14:08:45 rms-change max change #iterations 7.151139 316.2044 at 10iterations 3.845717 101.4633 at 20iterations 2.049520 54.52320 at 30iterations 1.089773 29.77198 at 40iterations 0.5786269 15.86212 at 50iterations 0.3053743 7.867366 at 60iterations 0.1613457 4.328037 at 70iterations 8.4822655E-02 2.283669 at 80iterations 4.4844650E-02 1.060447 at 90iterations 2.3569310E-02 0.5835056 at 100iterations 1.2400094E-02 0.3516521 at 110iterations 6.5210317E-03 0.1582756 at 120iterations 3.4325796E-03 8.4026337E-02 at 130iterations 1.7981161E-03 4.1854858E-02 at 140iterations 9.4633619E-04 2.2300720E-02 at 150iterations 4.9663195E-04 1.1329651E-02 at 160iterations 2.6125679E-04 6.4764619E-03 at 170iterations 1.3747084E-04 3.2367706E-03 at 180iterations finished qdiffx linear iterations at : 14:08:56 total time elapsed so far: 12.27000 # loops : 180 mean,max change (kT/e) : 1.3747084E-04 3.2367706E-03 energy calculations done at 12.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 14:08:57 12.456u 0.266s 0:13.08 97.1% 0+0k 0+0io 0pf+0w