Sat Oct 8 17:12:53 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 8 2011 at 17:12:53 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 = 3349 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: 0.5496032 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): 37.04700 97.42800 ymin,ymax (A): 14.59100 79.36500 zmin,zma (A): -22.99100 27.87200 x,y,z range (A): 60.38100 64.77400 50.86300 scale (grids/A): 0.5496032 object centre (A): 67.23750 46.97800 2.440500 number of atom coordinates read : 3349 total number of charged atoms : 3204 net assigned charge : -6.499982 assigned positive charge : 499.2826 centred at (gu) : 88.91102 90.59077 89.33715 assigned negative charge : -505.7838 centred at (gu) : 88.92957 90.55416 89.31427 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6645 nv = 96 ne = 84 npr = 67430 no. pairs analyzed = 67430 no. exposed pairs = 4166 no. arc points = 28687 no. surface atoms = 1416 nbur = 1933 mkacc time = 0.1400000 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 = 1.568000 m= 283 mr = 3590 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2961 ## 393 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8630 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.8229750E-10 -2.3249444E-10 midg,1,midg; midg,igrid,midg -6.8049988E-10 -1.7365598E-10 1,midg,midg; igrid,midg,midg -3.9726464E-10 -4.8370152E-10 gauss-seidel spectral radius is 0.9829556 estimated iterations to convergence 63 setup time was (sec) 0.5400000 now iterating at: 17:12:54 rms-change max change #iterations 7.9861768E-02 14.81254 at 10iterations 5.4702298E-03 0.9034214 at 20iterations 4.4016686E-04 7.5267792E-02 at 30iterations 6.7464374E-05 1.2126923E-02 at 40iterations 1.6851644E-05 3.2186508E-03 at 50iterations finished qdiffx linear iterations at : 17:12:57 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 1.6851644E-05 3.2186508E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 17:12:57 3.210u 0.165s 0:03.65 92.3% 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 8 2011 at 17:12:57 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 = 3349 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: 1.648810 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): 37.04700 97.42800 ymin,ymax (A): 14.59100 79.36500 zmin,zma (A): -22.99100 27.87200 x,y,z range (A): 60.38100 64.77400 50.86300 scale (grids/A): 1.648810 object centre (A): 67.23750 46.97800 2.440500 number of atom coordinates read : 3349 total number of charged atoms : 3204 net assigned charge : -6.499982 assigned positive charge : 499.2826 centred at (gu) : 86.73212 91.77115 88.01051 assigned negative charge : -505.7838 centred at (gu) : 86.78845 91.66193 87.94237 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28687 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23508 mr = 51481 m= 2436 mr = 16365 m= 89 mr = 1215 m= 0 mr = 5 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 532 time to turn everything in is 0.5100000 number of dielectric boundary points 30787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 327 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 24575 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) : 0.5496032 object centre at (A) : 67.23750 46.97800 2.440500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9278936E-03 -6.9475113E-03 midg,1,midg; midg,igrid,midg 2.8374083E-03 1.1848520E-02 1,midg,midg; igrid,midg,midg -2.1091422E-02 -3.9768452E-03 gauss-seidel spectral radius is 0.9982543 estimated iterations to convergence 190 setup time was (sec) 0.7800000 now iterating at: 17:12:58 rms-change max change #iterations 3.618767 159.8351 at 10iterations 1.534834 63.96294 at 20iterations 0.6501925 23.78519 at 30iterations 0.2766016 9.800316 at 40iterations 0.1178370 4.184752 at 50iterations 4.9896121E-02 1.733433 at 60iterations 2.1206945E-02 0.7022514 at 70iterations 9.0504615E-03 0.3070908 at 80iterations 3.8463578E-03 0.1280136 at 90iterations 1.6508951E-03 5.6928635E-02 at 100iterations 7.1690883E-04 2.5416374E-02 at 110iterations 3.1575561E-04 1.1175156E-02 at 120iterations finished qdiffx linear iterations at : 17:13:04 total time elapsed so far: 6.870000 # loops : 120 mean,max change (kT/e) : 3.1575561E-04 1.1175156E-02 energy calculations done at 6.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.040000 DelPhi exited at 17:13:05 7.042u 0.222s 0:07.56 96.0% 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 8 2011 at 17:13:05 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 = 3349 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: 2.473214 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): 37.04700 97.42800 ymin,ymax (A): 14.59100 79.36500 zmin,zma (A): -22.99100 27.87200 x,y,z range (A): 60.38100 64.77400 50.86300 scale (grids/A): 2.473214 object centre (A): 67.23750 46.97800 2.440500 number of atom coordinates read : 3349 total number of charged atoms : 3204 net assigned charge : -6.499982 assigned positive charge : 499.2826 centred at (gu) : 85.09811 92.65620 87.01577 assigned negative charge : -505.7838 centred at (gu) : 85.18259 92.49274 86.91348 start vw surface at 0.1800000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 171204 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28687 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 81765 mr = 125331 m= 23544 mr = 65470 m= 3987 mr = 17790 m= 344 mr = 2660 m= 9 mr = 165 m= 0 mr = 2 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 1752 time to turn everything in is 1.270000 number of dielectric boundary points 69435 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 25593 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) : 1.648810 object centre at (A) : 67.23750 46.97800 2.440500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4041784E-02 -7.6364242E-02 midg,1,midg; midg,igrid,midg 0.1193066 0.3493035 1,midg,midg; igrid,midg,midg -0.2478791 -3.5289053E-02 gauss-seidel spectral radius is 0.9991664 estimated iterations to convergence 274 setup time was (sec) 1.580000 now iterating at: 17:13:06 rms-change max change #iterations 9.311932 356.0903 at 10iterations 5.272246 127.0509 at 20iterations 2.968857 72.41648 at 30iterations 1.665231 34.17666 at 40iterations 0.9324571 18.49367 at 50iterations 0.5218841 10.25829 at 60iterations 0.2912266 5.816833 at 70iterations 0.1622860 3.157166 at 80iterations 9.0250626E-02 1.824389 at 90iterations 5.0163567E-02 0.9380913 at 100iterations 2.7900092E-02 0.5860214 at 110iterations 1.5546565E-02 0.3176727 at 120iterations 8.6398162E-03 0.1968384 at 130iterations 4.8161075E-03 8.8541985E-02 at 140iterations 2.6841857E-03 5.6001663E-02 at 150iterations 1.5040999E-03 2.7357697E-02 at 160iterations 8.4949267E-04 1.7477036E-02 at 170iterations 4.8585652E-04 9.2945099E-03 at 180iterations finished qdiffx linear iterations at : 17:13:16 total time elapsed so far: 11.18000 # loops : 180 mean,max change (kT/e) : 4.8585652E-04 9.2945099E-03 energy calculations done at 11.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.35000 DelPhi exited at 17:13:17 11.353u 0.202s 0:11.84 97.5% 0+0k 0+0io 0pf+0w