Sat Oct 15 12:42:57 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 Sat Oct 15 2011 at 12:43:01 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 = 5693 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 0.4816343 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): 3.922000 77.83700 ymin,ymax (A): 22.54700 85.59800 zmin,zma (A): 6.563000 70.54300 x,y,z range (A): 73.91500 63.05100 63.98000 scale (grids/A): 0.4816343 object centre (A): 40.87950 54.07250 38.55300 number of atom coordinates read : 5693 total number of charged atoms : 5528 net assigned charge : 1.514046 assigned positive charge : 857.1717 centred at (gu) : 89.55944 88.48025 89.27742 assigned negative charge : -855.6648 centred at (gu) : 89.38536 88.47362 89.18762 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8099 nv = 96 ne = 84 npr = 114610 no. pairs analyzed = 114610 no. exposed pairs = 7104 no. arc points = 49180 no. surface atoms = 2382 nbur = 3311 mkacc time = 0.2600000 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 = 1.792000 m= 267 mr = 4086 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4694 ## 832 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 11160 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4437866E-11 6.6062197E-11 midg,1,midg; midg,igrid,midg 2.1534443E-12 8.2621054E-12 1,midg,midg; igrid,midg,midg -1.6048024E-10 1.3124331E-10 gauss-seidel spectral radius is 0.9780299 estimated iterations to convergence 56 setup time was (sec) 0.7800000 now iterating at: 12:43:06 rms-change max change #iterations 5.4388415E-02 8.044746 at 10iterations 2.7855239E-03 0.4868889 at 20iterations 2.4790657E-04 5.3842545E-02 at 30iterations 5.2552758E-05 1.2340546E-02 at 40iterations 1.4130650E-05 3.0899048E-03 at 50iterations finished qdiffx linear iterations at : 12:43:17 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 1.4130650E-05 3.0899048E-03 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 12:43:19 4.432u 0.256s 0:18.30 25.5% 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 12:43:22 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 = 5693 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 1.444903 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): 3.922000 77.83700 ymin,ymax (A): 22.54700 85.59800 zmin,zma (A): 6.563000 70.54300 x,y,z range (A): 73.91500 63.05100 63.98000 scale (grids/A): 1.444903 object centre (A): 40.87950 54.07250 38.55300 number of atom coordinates read : 5693 total number of charged atoms : 5528 net assigned charge : 1.514046 assigned positive charge : 857.1717 centred at (gu) : 88.67632 85.43899 87.83013 assigned negative charge : -855.6648 centred at (gu) : 88.15550 85.42017 87.56245 start vw surface at 0.2300000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 93219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49180 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 24479 mr = 63259 m= 1573 mr = 15306 m= 21 mr = 578 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 914 time to turn everything in is 0.7100000 number of dielectric boundary points 40149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 843 ## 14 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 40688 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) : 0.4816343 object centre at (A) : 40.87950 54.07250 38.55300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5625865E-03 9.1361897E-03 midg,1,midg; midg,igrid,midg -1.0219106E-03 -3.1498254E-03 1,midg,midg; igrid,midg,midg -6.7673731E-03 2.1059774E-02 gauss-seidel spectral radius is 0.9979296 estimated iterations to convergence 175 setup time was (sec) 1.050000 now iterating at: 12:43:24 rms-change max change #iterations 3.642924 151.5253 at 10iterations 1.430246 47.69061 at 20iterations 0.5610072 19.17221 at 30iterations 0.2212235 7.237960 at 40iterations 8.6928912E-02 2.969116 at 50iterations 3.4247007E-02 1.084550 at 60iterations 1.3551885E-02 0.4439220 at 70iterations 5.3802677E-03 0.1632996 at 80iterations 2.1478012E-03 7.5374603E-02 at 90iterations 8.7307201E-04 2.9163361E-02 at 100iterations 3.7009429E-04 1.5581131E-02 at 110iterations 1.6838961E-04 6.1454773E-03 at 120iterations finished qdiffx linear iterations at : 12:43:47 total time elapsed so far: 9.860000 # loops : 120 mean,max change (kT/e) : 1.6838961E-04 6.1454773E-03 energy calculations done at 9.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.04000 DelPhi exited at 12:43:49 10.042u 0.320s 0:26.93 38.4% 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 12:43:49 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 = 5693 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 2.167354 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): 3.922000 77.83700 ymin,ymax (A): 22.54700 85.59800 zmin,zma (A): 6.563000 70.54300 x,y,z range (A): 73.91500 63.05100 63.98000 scale (grids/A): 2.167354 object centre (A): 40.87950 54.07250 38.55300 number of atom coordinates read : 5693 total number of charged atoms : 5528 net assigned charge : 1.514046 assigned positive charge : 857.1717 centred at (gu) : 88.01369 83.15829 86.74478 assigned negative charge : -855.6648 centred at (gu) : 87.23335 83.13018 86.34349 start vw surface at 0.2200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 218110 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49180 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 91477 mr = 156931 m= 19714 mr = 69178 m= 2039 mr = 13500 m= 57 mr = 1105 m= 0 mr = 9 time to grow re-entrant surface = 0.9899999 no. cavity mid-points inaccessible to solvent = 3093 time to turn everything in is 1.680000 number of dielectric boundary points 90674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 44005 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) : 1.444903 object centre at (A) : 40.87950 54.07250 38.55300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1313357 0.1614591 midg,1,midg; midg,igrid,midg -1.6652249E-02 -4.8765425E-02 1,midg,midg; igrid,midg,midg 2.5323331E-02 0.3610343 gauss-seidel spectral radius is 0.9991304 estimated iterations to convergence 268 setup time was (sec) 2.040000 now iterating at: 12:43:54 rms-change max change #iterations 10.33799 283.9536 at 10iterations 5.897954 141.6676 at 20iterations 3.337341 78.60733 at 30iterations 1.877401 39.67291 at 40iterations 1.053198 21.90634 at 50iterations 0.5881727 12.61641 at 60iterations 0.3279505 6.452471 at 70iterations 0.1826206 3.643609 at 80iterations 0.1011553 2.275486 at 90iterations 5.6124806E-02 1.105297 at 100iterations 3.1046359E-02 0.5846558 at 110iterations 1.7130572E-02 0.3693695 at 120iterations 9.4910357E-03 0.1804390 at 130iterations 5.2310894E-03 0.1018076 at 140iterations 2.8884492E-03 5.5225372E-02 at 150iterations 1.5950198E-03 2.9243469E-02 at 160iterations 8.7924377E-04 1.5468597E-02 at 170iterations 4.8608828E-04 8.2778931E-03 at 180iterations finished qdiffx linear iterations at : 12:44:23 total time elapsed so far: 16.58000 # loops : 180 mean,max change (kT/e) : 4.8608828E-04 8.2778931E-03 energy calculations done at 16.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.76000 DelPhi exited at 12:44:23 16.762u 0.310s 0:34.87 48.9% 0+0k 0+0io 0pf+0w