Sat Oct 15 12:01:32 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 12:01:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2298 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6447757 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): 6.369000 61.58200 ymin,ymax (A): -9.665000 33.70500 zmin,zma (A): -14.20300 41.00600 x,y,z range (A): 55.21300 43.37000 55.20900 scale (grids/A): 0.6447757 object centre (A): 33.97550 12.02000 13.40150 number of atom coordinates read : 2298 total number of charged atoms : 2164 net assigned charge : 9.000025 assigned positive charge : 331.6816 centred at (gu) : 90.82378 91.03721 89.38649 assigned negative charge : -322.6822 centred at (gu) : 90.84528 90.91782 89.41915 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6520 nv = 96 ne = 84 npr = 45886 no. pairs analyzed = 45886 no. exposed pairs = 3116 no. arc points = 21839 no. surface atoms = 1042 nbur = 1256 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 390 mr = 3301 m= 3 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.1800000 number of dielectric boundary points 3567 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2180 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7734 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0931024E-08 9.9273851E-09 midg,1,midg; midg,igrid,midg 1.3566908E-09 3.4657425E-08 1,midg,midg; igrid,midg,midg 1.4520881E-08 1.4739580E-08 gauss-seidel spectral radius is 0.9875200 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 12:01:32 rms-change max change #iterations 0.1349896 21.37472 at 10iterations 1.3707565E-02 1.781204 at 20iterations 1.3561256E-03 0.2066154 at 30iterations 1.3951059E-04 2.4022102E-02 at 40iterations 1.4401571E-05 2.0878315E-03 at 50iterations finished qdiffx linear iterations at : 12:01:35 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.4401571E-05 2.0878315E-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) 3.410000 DelPhi exited at 12:01:36 3.418u 0.194s 0:03.98 90.4% 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 12:01:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2298 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.934327 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): 6.369000 61.58200 ymin,ymax (A): -9.665000 33.70500 zmin,zma (A): -14.20300 41.00600 x,y,z range (A): 55.21300 43.37000 55.20900 scale (grids/A): 1.934327 object centre (A): 33.97550 12.02000 13.40150 number of atom coordinates read : 2298 total number of charged atoms : 2164 net assigned charge : 9.000025 assigned positive charge : 331.6816 centred at (gu) : 92.47115 93.11146 88.15905 assigned negative charge : -322.6822 centred at (gu) : 92.53604 92.75355 88.25750 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21839 grid for indexing accessible points = 1.400000 m= 25019 mr = 46386 m= 4362 mr = 17774 m= 362 mr = 2685 m= 6 mr = 143 m= 0 mr = 3 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 345 time to turn everything in is 0.3600000 number of dielectric boundary points 32842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17057 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) : 0.6447757 object centre at (A) : 33.97550 12.02000 13.40150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7744159E-02 4.0579155E-02 midg,1,midg; midg,igrid,midg -6.6717183E-03 3.2266185E-02 1,midg,midg; igrid,midg,midg 4.8201319E-02 3.5535544E-02 gauss-seidel spectral radius is 0.9986545 estimated iterations to convergence 216 setup time was (sec) 0.5700000 now iterating at: 12:01:36 rms-change max change #iterations 3.971884 201.6825 at 10iterations 1.865226 68.70142 at 20iterations 0.8769419 31.38332 at 30iterations 0.4118710 13.83981 at 40iterations 0.1935789 6.254148 at 50iterations 9.0651013E-02 2.967143 at 60iterations 4.2667292E-02 1.536693 at 70iterations 2.0105235E-02 0.6524546 at 80iterations 9.4392197E-03 0.3093958 at 90iterations 4.4373553E-03 0.1475163 at 100iterations 2.0905696E-03 6.5860748E-02 at 110iterations 9.8254881E-04 3.0807495E-02 at 120iterations finished qdiffx linear iterations at : 12:01:44 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 9.8254881E-04 3.0807495E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 12:01:44 7.923u 0.227s 0:08.45 96.3% 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 12:01:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2298 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: 2.901491 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): 6.369000 61.58200 ymin,ymax (A): -9.665000 33.70500 zmin,zma (A): -14.20300 41.00600 x,y,z range (A): 55.21300 43.37000 55.20900 scale (grids/A): 2.901491 object centre (A): 33.97550 12.02000 13.40150 number of atom coordinates read : 2298 total number of charged atoms : 2164 net assigned charge : 9.000025 assigned positive charge : 331.6816 centred at (gu) : 93.70680 94.66709 87.23863 assigned negative charge : -322.6822 centred at (gu) : 93.80418 94.13045 87.38623 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 161975 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21839 grid for indexing accessible points = 1.400000 m= 79740 mr = 113070 m= 29803 mr = 63492 m= 7888 mr = 23454 m= 1492 mr = 5810 m= 138 mr = 1050 m= 7 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 1306 time to turn everything in is 0.9500000 number of dielectric boundary points 74075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 17311 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) : 1.934327 object centre at (A) : 33.97550 12.02000 13.40150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4337170 0.4123060 midg,1,midg; midg,igrid,midg -6.4448848E-02 0.3260615 1,midg,midg; igrid,midg,midg 0.6820938 0.4039063 gauss-seidel spectral radius is 0.9992710 estimated iterations to convergence 292 setup time was (sec) 1.190000 now iterating at: 12:01:45 rms-change max change #iterations 9.397560 340.5475 at 10iterations 5.579957 132.9059 at 20iterations 3.267769 78.46548 at 30iterations 1.919111 42.67448 at 40iterations 1.115436 24.19928 at 50iterations 0.6497947 13.72973 at 60iterations 0.3776166 7.633202 at 70iterations 0.2192348 4.734179 at 80iterations 0.1266679 2.721895 at 90iterations 7.3541917E-02 1.523041 at 100iterations 4.2556841E-02 0.8159409 at 110iterations 2.4625147E-02 0.5184754 at 120iterations 1.4178561E-02 0.2731619 at 130iterations 8.2013654E-03 0.1563797 at 140iterations 4.7375616E-03 8.5827351E-02 at 150iterations 2.7386723E-03 5.0577879E-02 at 160iterations 1.5753813E-03 2.9221535E-02 at 170iterations 9.0973667E-04 1.6231537E-02 at 180iterations finished qdiffx linear iterations at : 12:01:57 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 9.0973667E-04 1.6231537E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 12:01:58 12.988u 0.250s 0:13.60 97.2% 0+0k 0+0io 0pf+0w