Tue Oct 11 06:06:13 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 06:06:13 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 = 2045 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7362065 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): -18.09900 30.25700 ymin,ymax (A): -11.70500 30.56600 zmin,zma (A): -8.532000 38.14700 x,y,z range (A): 48.35600 42.27100 46.67900 scale (grids/A): 0.7362065 object centre (A): 6.079000 9.430500 14.80750 number of atom coordinates read : 2045 total number of charged atoms : 1917 net assigned charge : 6.500009 assigned positive charge : 310.0090 centred at (gu) : 89.96363 89.87909 91.14875 assigned negative charge : -303.5092 centred at (gu) : 89.90107 89.79298 91.03243 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7644 nv = 96 ne = 84 npr = 40703 no. pairs analyzed = 40703 no. exposed pairs = 2530 no. arc points = 17408 no. surface atoms = 856 nbur = 1189 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 525 mr = 4410 m= 1 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2600000 number of dielectric boundary points 3662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1589 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8121 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7620904E-10 2.5662192E-07 midg,1,midg; midg,igrid,midg 2.7431476E-08 1.7636199E-07 1,midg,midg; igrid,midg,midg 4.8528918E-08 1.5861654E-07 gauss-seidel spectral radius is 0.9903739 estimated iterations to convergence 83 setup time was (sec) 0.5600000 now iterating at: 06:06:14 rms-change max change #iterations 0.2355340 32.62410 at 10iterations 3.1838335E-02 4.514687 at 20iterations 4.4056103E-03 0.5635262 at 30iterations 6.9492648E-04 8.3404541E-02 at 40iterations 1.5388640E-04 2.1717072E-02 at 50iterations finished qdiffx linear iterations at : 06:06:17 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 1.5388640E-04 2.1717072E-02 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 06:06:18 4.417u 0.417s 0:05.13 93.9% 0+0k 0+0io 6pf+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 06:06:18 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 = 2045 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.208619 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): -18.09900 30.25700 ymin,ymax (A): -11.70500 30.56600 zmin,zma (A): -8.532000 38.14700 x,y,z range (A): 48.35600 42.27100 46.67900 scale (grids/A): 2.208619 object centre (A): 6.079000 9.430500 14.80750 number of atom coordinates read : 2045 total number of charged atoms : 1917 net assigned charge : 6.500009 assigned positive charge : 310.0090 centred at (gu) : 89.89065 89.63718 93.44621 assigned negative charge : -303.5092 centred at (gu) : 89.70332 89.37910 93.09736 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17408 grid for indexing accessible points = 1.400000 m= 33903 mr = 57725 m= 7213 mr = 26152 m= 733 mr = 4957 m= 39 mr = 388 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 207 time to turn everything in is 0.6800000 number of dielectric boundary points 33475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15250 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) : 0.7362065 object centre at (A) : 6.079000 9.430500 14.80750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2967334E-02 4.8661452E-02 midg,1,midg; midg,igrid,midg 3.0589934E-02 2.8392443E-02 1,midg,midg; igrid,midg,midg 5.2041795E-02 3.3115461E-02 gauss-seidel spectral radius is 0.9989060 estimated iterations to convergence 239 setup time was (sec) 1.010000 now iterating at: 06:06:19 rms-change max change #iterations 4.868289 198.8500 at 10iterations 2.466250 78.50850 at 20iterations 1.256547 38.54601 at 30iterations 0.6389207 18.87200 at 40iterations 0.3228498 9.080048 at 50iterations 0.1645968 5.589844 at 60iterations 8.3293103E-02 2.359917 at 70iterations 4.2470433E-02 1.063919 at 80iterations 2.1723906E-02 0.7331009 at 90iterations 1.1055563E-02 0.3165131 at 100iterations 5.6768400E-03 0.1723205 at 110iterations 2.9362477E-03 8.5323334E-02 at 120iterations finished qdiffx linear iterations at : 06:06:29 total time elapsed so far: 10.67000 # loops : 120 mean,max change (kT/e) : 2.9362477E-03 8.5323334E-02 energy calculations done at 10.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.85000 DelPhi exited at 06:06:30 10.854u 0.468s 0:11.66 96.9% 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 Tue Oct 11 2011 at 06:06:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2045 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.312929 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): -18.09900 30.25700 ymin,ymax (A): -11.70500 30.56600 zmin,zma (A): -8.532000 38.14700 x,y,z range (A): 48.35600 42.27100 46.67900 scale (grids/A): 3.312929 object centre (A): 6.079000 9.430500 14.80750 number of atom coordinates read : 2045 total number of charged atoms : 1917 net assigned charge : 6.500009 assigned positive charge : 310.0090 centred at (gu) : 89.83612 89.45576 95.16926 assigned negative charge : -303.5092 centred at (gu) : 89.55507 89.06869 94.64611 start vw surface at 0.1100000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 186139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17408 grid for indexing accessible points = 1.400000 m= 103968 mr = 138743 m= 44856 mr = 87286 m= 13625 mr = 37312 m= 2963 mr = 10704 m= 400 mr = 2166 m= 26 mr = 244 m= 0 mr = 10 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 686 time to turn everything in is 2.110000 number of dielectric boundary points 75512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 15336 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) : 2.208619 object centre at (A) : 6.079000 9.430500 14.80750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4749169 0.4294272 midg,1,midg; midg,igrid,midg 0.2627478 0.1471477 1,midg,midg; igrid,midg,midg 0.3426959 0.1369081 gauss-seidel spectral radius is 0.9993165 estimated iterations to convergence 302 setup time was (sec) 2.490000 now iterating at: 06:06:33 rms-change max change #iterations 10.68109 305.1130 at 10iterations 6.363142 132.5501 at 20iterations 3.786714 70.84184 at 30iterations 2.252785 44.35717 at 40iterations 1.336932 23.11086 at 50iterations 0.7904710 12.64382 at 60iterations 0.4686274 9.024944 at 70iterations 0.2759916 4.801682 at 80iterations 0.1631766 2.783911 at 90iterations 9.6468113E-02 1.598057 at 100iterations 5.7010520E-02 0.9133263 at 110iterations 3.3784814E-02 0.6209488 at 120iterations 2.0131767E-02 0.3560143 at 130iterations 1.2072455E-02 0.2090855 at 140iterations 7.3861261E-03 0.1283493 at 150iterations 4.6569249E-03 9.7539902E-02 at 160iterations 3.0693528E-03 5.3695679E-02 at 170iterations 2.1500757E-03 3.9237976E-02 at 180iterations finished qdiffx linear iterations at : 06:06:49 total time elapsed so far: 18.34000 # loops : 180 mean,max change (kT/e) : 2.1500757E-03 3.9237976E-02 energy calculations done at 18.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.51000 DelPhi exited at 06:06:49 18.517u 0.488s 0:19.30 98.3% 0+0k 0+0io 0pf+0w