Sat Oct 8 23:50:28 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 8 2011 at 23:50:28 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2153 !!! WARNING: HIT 84 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6819531 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): -12.20300 40.00000 ymin,ymax (A): 14.17800 65.91800 zmin,zma (A): 3.129000 45.39300 x,y,z range (A): 52.20300 51.74000 42.26400 scale (grids/A): 0.6819531 object centre (A): 13.89850 40.04800 24.26100 number of atom coordinates read : 2153 total number of charged atoms : 2018 net assigned charge : 9.514023 assigned positive charge : 313.1648 centred at (gu) : 88.94773 88.62132 88.47774 assigned negative charge : -303.6513 centred at (gu) : 89.00178 88.59063 88.58572 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7061 nv = 96 ne = 84 npr = 42806 no. pairs analyzed = 42806 no. exposed pairs = 2893 no. arc points = 21077 no. surface atoms = 953 nbur = 1200 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 3705 m= 6 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 84 time to turn everything in is 0.1800000 number of dielectric boundary points 3750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1965 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7918 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5860109E-08 1.0283977E-08 midg,1,midg; midg,igrid,midg 4.4459409E-08 3.8518898E-08 1,midg,midg; igrid,midg,midg 6.9652067E-08 2.2854220E-08 gauss-seidel spectral radius is 0.9888225 estimated iterations to convergence 77 setup time was (sec) 0.3700000 now iterating at: 23:50:29 rms-change max change #iterations 0.1719151 23.81761 at 10iterations 1.9931639E-02 2.688303 at 20iterations 2.2244223E-03 0.3098183 at 30iterations 2.5558771E-04 3.4473419E-02 at 40iterations 2.9081632E-05 3.7393570E-03 at 50iterations finished qdiffx linear iterations at : 23:50:32 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.9081632E-05 3.7393570E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 23:50:32 3.429u 0.170s 0:03.92 91.5% 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 8 2011 at 23:50:32 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2153 !!! WARNING: HIT 84 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.045860 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): -12.20300 40.00000 ymin,ymax (A): 14.17800 65.91800 zmin,zma (A): 3.129000 45.39300 x,y,z range (A): 52.20300 51.74000 42.26400 scale (grids/A): 2.045860 object centre (A): 13.89850 40.04800 24.26100 number of atom coordinates read : 2153 total number of charged atoms : 2018 net assigned charge : 9.514023 assigned positive charge : 313.1648 centred at (gu) : 86.84293 85.86402 85.43318 assigned negative charge : -303.6513 centred at (gu) : 87.00548 85.77208 85.75715 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 74608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21077 grid for indexing accessible points = 1.400000 m= 27965 mr = 49978 m= 5442 mr = 20346 m= 524 mr = 3453 m= 13 mr = 273 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 2381 time to turn everything in is 0.3600000 number of dielectric boundary points 34502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 95 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 16019 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) : 0.6819531 object centre at (A) : 13.89850 40.04800 24.26100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9039157E-02 -1.4312940E-02 midg,1,midg; midg,igrid,midg 3.0892082E-02 6.1605018E-02 1,midg,midg; igrid,midg,midg 6.6429459E-02 4.3219279E-02 gauss-seidel spectral radius is 0.9987781 estimated iterations to convergence 227 setup time was (sec) 0.5900000 now iterating at: 23:50:33 rms-change max change #iterations 4.321123 219.7099 at 10iterations 2.100243 87.03712 at 20iterations 1.019831 34.23335 at 30iterations 0.4955854 16.02686 at 40iterations 0.2412308 7.562462 at 50iterations 0.1170426 3.905958 at 60iterations 5.7229385E-02 1.804955 at 70iterations 2.7989265E-02 0.9096451 at 80iterations 1.3589115E-02 0.4126835 at 90iterations 6.6226618E-03 0.2010517 at 100iterations 3.2371767E-03 9.8075867E-02 at 110iterations 1.5795442E-03 4.9951553E-02 at 120iterations finished qdiffx linear iterations at : 23:50:40 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 1.5795442E-03 4.9951553E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 23:50:41 7.973u 0.208s 0:08.50 96.1% 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 8 2011 at 23:50:41 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2153 !!! WARNING: HIT 84 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.068789 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): -12.20300 40.00000 ymin,ymax (A): 14.17800 65.91800 zmin,zma (A): 3.129000 45.39300 x,y,z range (A): 52.20300 51.74000 42.26400 scale (grids/A): 3.068789 object centre (A): 13.89850 40.04800 24.26100 number of atom coordinates read : 2153 total number of charged atoms : 2018 net assigned charge : 9.514023 assigned positive charge : 313.1648 centred at (gu) : 85.26443 83.79579 83.14975 assigned negative charge : -303.6513 centred at (gu) : 85.50822 83.65813 83.63570 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 171944 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21077 grid for indexing accessible points = 1.400000 m= 87509 mr = 121293 m= 34991 mr = 70688 m= 10181 mr = 27893 m= 2027 mr = 7613 m= 249 mr = 1477 m= 10 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 7961 time to turn everything in is 0.9800000 number of dielectric boundary points 77807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 16144 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) : 2.045860 object centre at (A) : 13.89850 40.04800 24.26100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3069944 -0.1702486 midg,1,midg; midg,igrid,midg 0.3297932 0.6964096 1,midg,midg; igrid,midg,midg 0.5121344 0.3935973 gauss-seidel spectral radius is 0.9993073 estimated iterations to convergence 300 setup time was (sec) 1.220000 now iterating at: 23:50:42 rms-change max change #iterations 10.02193 395.8900 at 10iterations 5.983479 158.7783 at 20iterations 3.567862 71.43057 at 30iterations 2.122641 42.82163 at 40iterations 1.257341 24.96395 at 50iterations 0.7401721 14.43894 at 60iterations 0.4371785 9.232980 at 70iterations 0.2569805 4.922333 at 80iterations 0.1513432 2.805164 at 90iterations 8.8608019E-02 1.640246 at 100iterations 5.2052304E-02 1.137180 at 110iterations 3.0477338E-02 0.5718994 at 120iterations 1.7887495E-02 0.3024721 at 130iterations 1.0471610E-02 0.1867857 at 140iterations 6.1409473E-03 0.1218307 at 150iterations 3.5927328E-03 6.7199707E-02 at 160iterations 2.1086843E-03 3.8391113E-02 at 170iterations 1.2308175E-03 2.1350861E-02 at 180iterations finished qdiffx linear iterations at : 23:50:54 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 1.2308175E-03 2.1350861E-02 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 23:50:54 13.031u 0.214s 0:13.51 98.0% 0+0k 0+0io 0pf+0w