Sat Oct 15 13:46:57 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 13:46:59 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: GLM 776 has a net charge of -0.0940 !!! WARNING: SEP 810 has a net charge of -0.4750 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: 0.6717362 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): -3.322000 49.67500 ymin,ymax (A): 41.91600 88.64900 zmin,zma (A): -4.612000 41.60900 x,y,z range (A): 52.99700 46.73300 46.22100 scale (grids/A): 0.6717362 object centre (A): 23.17650 65.28250 18.49850 number of atom coordinates read : 2318 total number of charged atoms : 2213 net assigned charge : -1.569000 assigned positive charge : 340.3472 centred at (gu) : 90.63419 90.89809 89.90636 assigned negative charge : -341.9169 centred at (gu) : 90.52819 91.00457 89.97737 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7164 nv = 96 ne = 84 npr = 47365 no. pairs analyzed = 47365 no. exposed pairs = 2895 no. arc points = 20424 no. surface atoms = 988 nbur = 1330 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 453 mr = 3967 m= 3 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3580 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1908 ## 138 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8349 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1370040E-08 -2.1675174E-08 midg,1,midg; midg,igrid,midg 1.5959756E-08 -3.6839953E-08 1,midg,midg; igrid,midg,midg -2.6706005E-08 2.1958638E-08 gauss-seidel spectral radius is 0.9884890 estimated iterations to convergence 76 setup time was (sec) 0.4200000 now iterating at: 13:47:00 rms-change max change #iterations 0.1671142 25.16703 at 10iterations 1.8502634E-02 2.641983 at 20iterations 2.0151413E-03 0.2778072 at 30iterations 2.2339659E-04 3.5358429E-02 at 40iterations 2.4864879E-05 4.0645599E-03 at 50iterations finished qdiffx linear iterations at : 13:47:06 total time elapsed so far: 3.710000 # loops : 50 mean,max change (kT/e) : 2.4864879E-05 4.0645599E-03 energy calculations done at 3.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.850000 DelPhi exited at 13:47:08 3.856u 0.274s 0:08.88 46.3% 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 13:47:08 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: GLM 776 has a net charge of -0.0940 !!! WARNING: SEP 810 has a net charge of -0.4750 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: 2.015208 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): -3.322000 49.67500 ymin,ymax (A): 41.91600 88.64900 zmin,zma (A): -4.612000 41.60900 x,y,z range (A): 52.99700 46.73300 46.22100 scale (grids/A): 2.015208 object centre (A): 23.17650 65.28250 18.49850 number of atom coordinates read : 2318 total number of charged atoms : 2213 net assigned charge : -1.569000 assigned positive charge : 340.3472 centred at (gu) : 91.90218 92.69381 89.71861 assigned negative charge : -341.9169 centred at (gu) : 91.58449 93.01370 89.93202 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76351 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20424 grid for indexing accessible points = 1.400000 m= 28461 mr = 53060 m= 5199 mr = 21080 m= 400 mr = 3307 m= 12 mr = 188 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1256 time to turn everything in is 0.3900000 number of dielectric boundary points 32788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 17550 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) : 0.6717362 object centre at (A) : 23.17650 65.28250 18.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9719577E-03 -3.9727107E-02 midg,1,midg; midg,igrid,midg 1.7708322E-02 -4.3402985E-02 1,midg,midg; igrid,midg,midg 6.1357920E-03 6.6326909E-02 gauss-seidel spectral radius is 0.9987515 estimated iterations to convergence 224 setup time was (sec) 0.6500000 now iterating at: 13:47:09 rms-change max change #iterations 4.396159 208.7375 at 10iterations 2.125879 76.47246 at 20iterations 1.031162 31.20215 at 30iterations 0.4971150 15.90628 at 40iterations 0.2407063 7.002606 at 50iterations 0.1167389 4.057213 at 60iterations 5.6449499E-02 1.616718 at 70iterations 2.7269213E-02 0.8612804 at 80iterations 1.3245231E-02 0.4108076 at 90iterations 6.4020636E-03 0.2075262 at 100iterations 3.1090782E-03 0.1001768 at 110iterations 1.5063578E-03 4.1790485E-02 at 120iterations finished qdiffx linear iterations at : 13:47:27 total time elapsed so far: 9.170000 # loops : 120 mean,max change (kT/e) : 1.5063578E-03 4.1790485E-02 energy calculations done at 9.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.290000 DelPhi exited at 13:47:28 9.292u 0.334s 0:20.43 47.0% 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 13:47:29 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: GLM 776 has a net charge of -0.0940 !!! WARNING: SEP 810 has a net charge of -0.4750 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: 3.022813 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): -3.322000 49.67500 ymin,ymax (A): 41.91600 88.64900 zmin,zma (A): -4.612000 41.60900 x,y,z range (A): 52.99700 46.73300 46.22100 scale (grids/A): 3.022813 object centre (A): 23.17650 65.28250 18.49850 number of atom coordinates read : 2318 total number of charged atoms : 2213 net assigned charge : -1.569000 assigned positive charge : 340.3472 centred at (gu) : 92.85329 94.04071 89.57780 assigned negative charge : -341.9169 centred at (gu) : 92.37675 94.52058 89.89796 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 176651 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20424 grid for indexing accessible points = 1.400000 m= 89923 mr = 128764 m= 35375 mr = 73652 m= 9590 mr = 28563 m= 1654 mr = 7271 m= 159 mr = 1137 m= 5 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 4326 time to turn everything in is 1.100000 number of dielectric boundary points 73870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 17704 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) : 2.015208 object centre at (A) : 23.17650 65.28250 18.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2514186E-03 -0.3108271 midg,1,midg; midg,igrid,midg 0.2864021 -0.4331687 1,midg,midg; igrid,midg,midg 0.1347877 0.6750828 gauss-seidel spectral radius is 0.9992836 estimated iterations to convergence 295 setup time was (sec) 1.410000 now iterating at: 13:47:34 rms-change max change #iterations 10.10828 407.0258 at 10iterations 5.925190 118.0036 at 20iterations 3.475265 70.25139 at 30iterations 2.026050 39.80207 at 40iterations 1.184186 23.95490 at 50iterations 0.6899248 11.57384 at 60iterations 0.4025292 7.905645 at 70iterations 0.2342206 5.527900 at 80iterations 0.1362415 2.519072 at 90iterations 7.9129584E-02 1.335718 at 100iterations 4.5904301E-02 0.7575927 at 110iterations 2.6720064E-02 0.4818902 at 120iterations 1.5504763E-02 0.2537001 at 130iterations 8.9961886E-03 0.1653013 at 140iterations 5.2222703E-03 9.2851639E-02 at 150iterations 3.0267409E-03 5.5420876E-02 at 160iterations 1.7546637E-03 2.9624939E-02 at 170iterations 1.0187393E-03 1.7372131E-02 at 180iterations finished qdiffx linear iterations at : 13:48:00 total time elapsed so far: 15.33000 # loops : 180 mean,max change (kT/e) : 1.0187393E-03 1.7372131E-02 energy calculations done at 15.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.47000 DelPhi exited at 13:48:00 15.475u 0.325s 0:31.90 49.4% 0+0k 0+0io 0pf+0w