Sat Oct 15 13:14:19 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+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 Sat Oct 15 2011 at 13:14:19 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5496 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3991 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4862458 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): 7.796999 61.74600 ymin,ymax (A): 53.30000 126.5140 zmin,zma (A): 29.05700 96.74600 x,y,z range (A): 53.94900 73.21400 67.68900 scale (grids/A): 0.4862458 object centre (A): 34.77150 89.90700 62.90150 number of atom coordinates read : 5496 total number of charged atoms : 5331 net assigned charge : 5.100036 assigned positive charge : 856.6194 centred at (gu) : 89.52839 90.28215 90.57582 assigned negative charge : -851.5269 centred at (gu) : 89.54314 90.25040 90.44170 start vw surface at 0.1900000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7674 nv = 96 ne = 84 npr = 112016 no. pairs analyzed = 112016 no. exposed pairs = 6544 no. arc points = 45038 no. surface atoms = 2197 nbur = 3299 mkacc time = 0.3000000 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 = 1.764000 m= 231 mr = 3981 m= 0 mr = 4 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.5800000 number of dielectric boundary points 3920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4269 ## 733 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 10698 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0171162E-10 1.8633144E-10 midg,1,midg; midg,igrid,midg -1.0027008E-11 5.9362598E-11 1,midg,midg; igrid,midg,midg 4.2557926E-11 6.0882354E-12 gauss-seidel spectral radius is 0.9784158 estimated iterations to convergence 56 setup time was (sec) 0.9200000 now iterating at: 13:14:20 rms-change max change #iterations 5.6076180E-02 10.39082 at 10iterations 3.9394987E-03 0.5897560 at 20iterations 8.3402504E-04 0.1171093 at 30iterations 2.6266047E-04 3.9553642E-02 at 40iterations 8.6666158E-05 1.4765739E-02 at 50iterations finished qdiffx linear iterations at : 13:14:25 total time elapsed so far: 5.490000 # loops : 50 mean,max change (kT/e) : 8.6666158E-05 1.4765739E-02 energy calculations done at 5.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.670000 DelPhi exited at 13:14:25 5.672u 0.447s 0:06.54 93.4% 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 Sat Oct 15 2011 at 13:14:25 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5496 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3991 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.458737 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): 7.796999 61.74600 ymin,ymax (A): 53.30000 126.5140 zmin,zma (A): 29.05700 96.74600 x,y,z range (A): 53.94900 73.21400 67.68900 scale (grids/A): 1.458737 object centre (A): 34.77150 89.90700 62.90150 number of atom coordinates read : 5496 total number of charged atoms : 5331 net assigned charge : 5.100036 assigned positive charge : 856.6194 centred at (gu) : 88.58332 90.84487 91.72596 assigned negative charge : -851.5269 centred at (gu) : 88.62920 90.75099 91.32509 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 88850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45038 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 23702 mr = 61521 m= 1627 mr = 15437 m= 24 mr = 612 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1684 time to turn everything in is 0.7800000 number of dielectric boundary points 36633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 691 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 39284 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) : 0.4862458 object centre at (A) : 34.77150 89.90700 62.90150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0781752E-02 1.3433902E-02 midg,1,midg; midg,igrid,midg -3.6429011E-03 5.4053584E-04 1,midg,midg; igrid,midg,midg 3.4008948E-03 2.0262036E-03 gauss-seidel spectral radius is 0.9979360 estimated iterations to convergence 175 setup time was (sec) 1.180000 now iterating at: 13:14:27 rms-change max change #iterations 3.713161 150.3550 at 10iterations 1.455989 48.17008 at 20iterations 0.5727501 18.74694 at 30iterations 0.2263700 7.661915 at 40iterations 8.9460939E-02 2.884475 at 50iterations 3.5387959E-02 1.100398 at 60iterations 1.4069109E-02 0.4802742 at 70iterations 5.6747776E-03 0.2004204 at 80iterations 2.3807292E-03 8.3267212E-02 at 90iterations 1.0818905E-03 3.4484863E-02 at 100iterations 5.5236142E-04 1.9510269E-02 at 110iterations 3.2103970E-04 1.0334253E-02 at 120iterations finished qdiffx linear iterations at : 13:14:39 total time elapsed so far: 13.13000 # loops : 120 mean,max change (kT/e) : 3.2103970E-04 1.0334253E-02 energy calculations done at 13.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 13:14:40 13.314u 0.507s 0:14.25 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 Sat Oct 15 2011 at 13:14:40 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5496 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3991 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.188106 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): 7.796999 61.74600 ymin,ymax (A): 53.30000 126.5140 zmin,zma (A): 29.05700 96.74600 x,y,z range (A): 53.94900 73.21400 67.68900 scale (grids/A): 2.188106 object centre (A): 34.77150 89.90700 62.90150 number of atom coordinates read : 5496 total number of charged atoms : 5331 net assigned charge : 5.100036 assigned positive charge : 856.6194 centred at (gu) : 87.87474 91.26685 92.58862 assigned negative charge : -851.5269 centred at (gu) : 87.94382 91.12613 91.98753 start vw surface at 0.1800000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 207765 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45038 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 87521 mr = 151655 m= 19512 mr = 67796 m= 2130 mr = 13743 m= 69 mr = 1170 m= 0 mr = 12 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 5568 time to turn everything in is 1.850000 number of dielectric boundary points 82621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 42426 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) : 1.458737 object centre at (A) : 34.77150 89.90700 62.90150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1789992 0.2230127 midg,1,midg; midg,igrid,midg -0.1216570 -9.3207834E-03 1,midg,midg; igrid,midg,midg 6.7503102E-02 4.6514846E-02 gauss-seidel spectral radius is 0.9991140 estimated iterations to convergence 265 setup time was (sec) 2.260000 now iterating at: 13:14:42 rms-change max change #iterations 10.34174 264.8155 at 10iterations 5.795621 131.4626 at 20iterations 3.227932 68.69465 at 30iterations 1.788590 38.61781 at 40iterations 0.9857556 20.90355 at 50iterations 0.5434737 10.60030 at 60iterations 0.2992858 6.700499 at 70iterations 0.1640435 2.899555 at 80iterations 9.0059787E-02 1.615029 at 90iterations 4.9200688E-02 0.9243393 at 100iterations 2.6938675E-02 0.5540686 at 110iterations 1.4738962E-02 0.2812243 at 120iterations 8.0670156E-03 0.1599045 at 130iterations 4.4190721E-03 8.1472397E-02 at 140iterations 2.4122379E-03 4.3701172E-02 at 150iterations 1.3230657E-03 2.5003433E-02 at 160iterations 7.2634249E-04 1.3366699E-02 at 170iterations 3.9993483E-04 7.4634552E-03 at 180iterations finished qdiffx linear iterations at : 13:15:02 total time elapsed so far: 22.01000 # loops : 180 mean,max change (kT/e) : 3.9993483E-04 7.4634552E-03 energy calculations done at 22.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.17000 DelPhi exited at 13:15:03 22.176u 0.588s 0:23.11 98.4% 0+0k 0+0io 0pf+0w