Sun Oct 9 17:36:50 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 Sun Oct 9 2011 at 17:36:50 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3208 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5739899 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): -11.06500 50.95700 ymin,ymax (A): -12.34200 40.78000 zmin,zma (A): 19.77300 76.03300 x,y,z range (A): 62.02200 53.12200 56.26001 scale (grids/A): 0.5739899 object centre (A): 19.94600 14.21900 47.90300 number of atom coordinates read : 3208 total number of charged atoms : 3061 net assigned charge : 3.621018 assigned positive charge : 494.9659 centred at (gu) : 90.78865 89.70121 87.76241 assigned negative charge : -491.3461 centred at (gu) : 90.66860 89.83044 87.68382 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7128 nv = 96 ne = 84 npr = 62040 no. pairs analyzed = 62040 no. exposed pairs = 4369 no. arc points = 31053 no. surface atoms = 1458 nbur = 1750 mkacc time = 0.1500000 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 = 1.484000 m= 340 mr = 3569 m= 0 mr = 16 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3883 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2940 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8788 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6150090E-09 1.2963515E-09 midg,1,midg; midg,igrid,midg 3.3979226E-09 -1.8072546E-09 1,midg,midg; igrid,midg,midg -1.4495276E-09 3.6082852E-09 gauss-seidel spectral radius is 0.9843602 estimated iterations to convergence 66 setup time was (sec) 0.5800000 now iterating at: 17:36:50 rms-change max change #iterations 9.7368881E-02 15.41920 at 10iterations 7.2647491E-03 1.035166 at 20iterations 5.7202147E-04 9.9208832E-02 at 30iterations 4.9196206E-05 6.8130493E-03 at 40iterations 7.9562906E-06 1.0719299E-03 at 50iterations finished qdiffx linear iterations at : 17:36:53 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 7.9562906E-06 1.0719299E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 17:36:54 3.399u 0.164s 0:03.86 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 Sun Oct 9 2011 at 17:36:54 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3208 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.721969 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): -11.06500 50.95700 ymin,ymax (A): -12.34200 40.78000 zmin,zma (A): 19.77300 76.03300 x,y,z range (A): 62.02200 53.12200 56.26001 scale (grids/A): 1.721969 object centre (A): 19.94600 14.21900 47.90300 number of atom coordinates read : 3208 total number of charged atoms : 3061 net assigned charge : 3.621018 assigned positive charge : 494.9659 centred at (gu) : 92.36510 89.10294 83.28645 assigned negative charge : -491.3461 centred at (gu) : 92.00546 89.49083 83.05087 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 77143 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31053 grid for indexing accessible points = 1.400000 m= 25589 mr = 51175 m= 3129 mr = 17166 m= 125 mr = 1506 m= 0 mr = 14 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 36125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 23660 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) : 0.5739899 object centre at (A) : 19.94600 14.21900 47.90300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3800854E-03 6.3808928E-03 midg,1,midg; midg,igrid,midg 2.3283541E-02 -1.1659551E-02 1,midg,midg; igrid,midg,midg -7.7981786E-03 2.1838542E-02 gauss-seidel spectral radius is 0.9984040 estimated iterations to convergence 199 setup time was (sec) 0.8700000 now iterating at: 17:36:55 rms-change max change #iterations 3.991450 192.8814 at 10iterations 1.757220 70.97904 at 20iterations 0.7788483 29.34882 at 30iterations 0.3436097 13.00389 at 40iterations 0.1518757 4.744324 at 50iterations 6.7110069E-02 2.311205 at 60iterations 2.9716451E-02 1.037677 at 70iterations 1.3141945E-02 0.4623594 at 80iterations 5.8029266E-03 0.2138214 at 90iterations 2.5831889E-03 8.9417934E-02 at 100iterations 1.1805377E-03 4.0249825E-02 at 110iterations 5.6955306E-04 2.2709846E-02 at 120iterations finished qdiffx linear iterations at : 17:37:01 total time elapsed so far: 7.380000 # loops : 120 mean,max change (kT/e) : 5.6955306E-04 2.2709846E-02 energy calculations done at 7.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 17:37:02 7.572u 0.171s 0:08.01 96.6% 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 Sun Oct 9 2011 at 17:37:02 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3208 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.582954 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): -11.06500 50.95700 ymin,ymax (A): -12.34200 40.78000 zmin,zma (A): 19.77300 76.03300 x,y,z range (A): 62.02200 53.12200 56.26001 scale (grids/A): 2.582954 object centre (A): 19.94600 14.21900 47.90300 number of atom coordinates read : 3208 total number of charged atoms : 3061 net assigned charge : 3.621018 assigned positive charge : 494.9659 centred at (gu) : 93.54737 88.65423 79.92940 assigned negative charge : -491.3461 centred at (gu) : 93.00813 89.23606 79.57632 start vw surface at 0.2000000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 178665 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31053 grid for indexing accessible points = 1.400000 m= 85269 mr = 125471 m= 27070 mr = 66204 m= 5134 mr = 20054 m= 465 mr = 3217 m= 11 mr = 223 m= 0 mr = 1 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.480000 number of dielectric boundary points 81444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 24477 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) : 1.721969 object centre at (A) : 19.94600 14.21900 47.90300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7118548E-02 7.5003110E-02 midg,1,midg; midg,igrid,midg 0.3058295 -0.2207613 1,midg,midg; igrid,midg,midg 0.1080992 0.2827403 gauss-seidel spectral radius is 0.9992199 estimated iterations to convergence 283 setup time was (sec) 1.790000 now iterating at: 17:37:04 rms-change max change #iterations 10.22777 419.6336 at 10iterations 6.034295 141.4320 at 20iterations 3.507261 89.46291 at 30iterations 2.032336 46.40007 at 40iterations 1.168324 25.44445 at 50iterations 0.6721996 13.85347 at 60iterations 0.3839891 8.195921 at 70iterations 0.2198247 5.133915 at 80iterations 0.1253228 2.463180 at 90iterations 7.1395829E-02 1.721517 at 100iterations 4.0689215E-02 0.8275375 at 110iterations 2.3130719E-02 0.4503174 at 120iterations 1.3171442E-02 0.2742453 at 130iterations 7.4928207E-03 0.1419227 at 140iterations 4.2886869E-03 8.3715439E-02 at 150iterations 2.4665273E-03 5.1684380E-02 at 160iterations 1.4416446E-03 2.7692795E-02 at 170iterations 8.7375334E-04 1.8329144E-02 at 180iterations finished qdiffx linear iterations at : 17:37:14 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 8.7375334E-04 1.8329144E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.61000 DelPhi exited at 17:37:15 12.617u 0.177s 0:13.13 97.3% 0+0k 0+0io 0pf+0w