Mon Oct 10 11:09:35 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 Mon Oct 10 2011 at 11:09:35 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7456590 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): -22.23700 24.31100 ymin,ymax (A): -7.941000 36.11400 zmin,zma (A): -3.478000 44.26500 x,y,z range (A): 46.54800 44.05500 47.74300 scale (grids/A): 0.7456590 object centre (A): 1.037000 14.08650 20.39350 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.271990 assigned positive charge : 316.2599 centred at (gu) : 89.47541 90.43147 90.12794 assigned negative charge : -321.5320 centred at (gu) : 89.48473 90.48779 90.25735 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8117 nv = 96 ne = 84 npr = 43546 no. pairs analyzed = 43546 no. exposed pairs = 2671 no. arc points = 19011 no. surface atoms = 902 nbur = 1205 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 549 mr = 4522 m= 6 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 0.3000000 number of dielectric boundary points 4016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1503 ## 126 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8408 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0774616E-08 -2.6042105E-07 midg,1,midg; midg,igrid,midg -3.7556337E-08 -1.8312760E-07 1,midg,midg; igrid,midg,midg -1.0286615E-07 -1.0469370E-07 gauss-seidel spectral radius is 0.9906274 estimated iterations to convergence 84 setup time was (sec) 0.5600000 now iterating at: 11:09:36 rms-change max change #iterations 0.2500456 33.56138 at 10iterations 3.4599151E-02 5.888721 at 20iterations 4.7224965E-03 0.6263037 at 30iterations 6.3992484E-04 7.9745293E-02 at 40iterations 8.8974899E-05 1.2826443E-02 at 50iterations finished qdiffx linear iterations at : 11:09:39 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 8.8974899E-05 1.2826443E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 11:09:40 3.621u 0.202s 0:04.14 92.2% 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 Mon Oct 10 2011 at 11:09:40 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.236977 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): -22.23700 24.31100 ymin,ymax (A): -7.941000 36.11400 zmin,zma (A): -3.478000 44.26500 x,y,z range (A): 46.54800 44.05500 47.74300 scale (grids/A): 2.236977 object centre (A): 1.037000 14.08650 20.39350 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.271990 assigned positive charge : 316.2599 centred at (gu) : 88.42620 91.29444 90.38374 assigned negative charge : -321.5320 centred at (gu) : 88.45419 91.46342 90.77219 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 85007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19011 grid for indexing accessible points = 1.400000 m= 34448 mr = 58885 m= 7591 mr = 26359 m= 860 mr = 5354 m= 26 mr = 523 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1572 time to turn everything in is 0.6600000 number of dielectric boundary points 36808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 51 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 15694 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) : 0.7456590 object centre at (A) : 1.037000 14.08650 20.39350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0806266E-03 -0.1159268 midg,1,midg; midg,igrid,midg -2.7997741E-02 -3.7191585E-02 1,midg,midg; igrid,midg,midg -3.2313990E-03 1.5030892E-03 gauss-seidel spectral radius is 0.9989397 estimated iterations to convergence 243 setup time was (sec) 0.9800000 now iterating at: 11:09:41 rms-change max change #iterations 5.139790 194.2155 at 10iterations 2.625368 83.54968 at 20iterations 1.340576 41.38496 at 30iterations 0.6890504 19.83901 at 40iterations 0.3517635 11.07368 at 50iterations 0.1806053 5.296507 at 60iterations 9.2278726E-02 2.755321 at 70iterations 4.7202107E-02 1.387732 at 80iterations 2.4248160E-02 0.7014771 at 90iterations 1.2388474E-02 0.3789539 at 100iterations 6.3469051E-03 0.1764832 at 110iterations 3.2476571E-03 9.6661568E-02 at 120iterations finished qdiffx linear iterations at : 11:09:48 total time elapsed so far: 8.120000 # loops : 120 mean,max change (kT/e) : 3.2476571E-03 9.6661568E-02 energy calculations done at 8.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.300000 DelPhi exited at 11:09:49 8.301u 0.251s 0:08.96 95.4% 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 Mon Oct 10 2011 at 11:09:49 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.355465 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): -22.23700 24.31100 ymin,ymax (A): -7.941000 36.11400 zmin,zma (A): -3.478000 44.26500 x,y,z range (A): 46.54800 44.05500 47.74300 scale (grids/A): 3.355465 object centre (A): 1.037000 14.08650 20.39350 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.271990 assigned positive charge : 316.2599 centred at (gu) : 87.63926 91.94160 90.57565 assigned negative charge : -321.5320 centred at (gu) : 87.68134 92.19514 91.15821 start vw surface at 0.1400000 fill in re-entrant regions at 0.9900000 boundary points on vw surface= 195360 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19011 grid for indexing accessible points = 1.400000 m= 105178 mr = 141330 m= 45620 mr = 87629 m= 14540 mr = 37965 m= 3583 mr = 11683 m= 479 mr = 2839 m= 22 mr = 344 m= 0 mr = 3 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 5428 time to turn everything in is 2.140000 number of dielectric boundary points 82989 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.280000 number of grid points assigned charge 15752 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) : 2.236977 object centre at (A) : 1.037000 14.08650 20.39350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6292149E-03 -1.111168 midg,1,midg; midg,igrid,midg -0.2506709 -0.1981986 1,midg,midg; igrid,midg,midg -2.7029296E-02 -0.1507870 gauss-seidel spectral radius is 0.9993236 estimated iterations to convergence 303 setup time was (sec) 2.450000 now iterating at: 11:09:51 rms-change max change #iterations 11.09841 420.2289 at 10iterations 6.536306 112.2217 at 20iterations 3.864196 64.44391 at 30iterations 2.274221 37.78522 at 40iterations 1.339865 22.79510 at 50iterations 0.7905880 12.42199 at 60iterations 0.4662075 7.516878 at 70iterations 0.2738558 4.863123 at 80iterations 0.1611920 2.547382 at 90iterations 9.4826251E-02 1.514395 at 100iterations 5.5761978E-02 0.8611374 at 110iterations 3.2731522E-02 0.5331583 at 120iterations 1.9294679E-02 0.3454897 at 130iterations 1.1313279E-02 0.1770027 at 140iterations 6.6667623E-03 0.1072316 at 150iterations 3.9277868E-03 6.7158937E-02 at 160iterations 2.3095959E-03 3.6012650E-02 at 170iterations 1.3559164E-03 2.2755623E-02 at 180iterations finished qdiffx linear iterations at : 11:10:02 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 1.3559164E-03 2.2755623E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 11:10:02 12.871u 0.209s 0:13.35 97.9% 0+0k 0+0io 0pf+0w