Sat Oct 8 18:21:48 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 18:21:48 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3759 !!! WARNING: GLM 77 has a net charge of -0.0940 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: 0.5506403 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): -3.289000 60.40500 ymin,ymax (A): -18.55700 44.40500 zmin,zma (A): -5.537000 59.11500 x,y,z range (A): 63.69400 62.96200 64.65200 scale (grids/A): 0.5506403 object centre (A): 28.55800 12.92400 26.78900 number of atom coordinates read : 3759 total number of charged atoms : 3605 net assigned charge : -8.093967 assigned positive charge : 571.5262 centred at (gu) : 89.13384 86.75104 90.48790 assigned negative charge : -579.6228 centred at (gu) : 89.19609 86.73530 90.48077 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7433 nv = 96 ne = 84 npr = 75892 no. pairs analyzed = 75892 no. exposed pairs = 4888 no. arc points = 34338 no. surface atoms = 1625 nbur = 2134 mkacc time = 0.2200000 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= 310 mr = 3832 m= 0 mr = 13 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 3898 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3469 ## 460 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 9708 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9480776E-10 -5.8773864E-10 midg,1,midg; midg,igrid,midg -1.6773445E-09 -2.0699724E-10 1,midg,midg; igrid,midg,midg 4.5717926E-11 -9.9847797E-10 gauss-seidel spectral radius is 0.9830548 estimated iterations to convergence 63 setup time was (sec) 0.7400000 now iterating at: 18:21:49 rms-change max change #iterations 8.6821713E-02 15.09811 at 10iterations 6.2986240E-03 0.9098349 at 20iterations 6.1801571E-04 0.1076317 at 30iterations 1.4313817E-04 2.7157784E-02 at 40iterations 4.3388678E-05 8.3551407E-03 at 50iterations finished qdiffx linear iterations at : 18:21:52 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 4.3388678E-05 8.3551407E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 18:21:53 4.210u 0.255s 0:04.79 93.1% 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 18:21:53 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3759 !!! WARNING: GLM 77 has a net charge of -0.0940 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: 1.651921 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): -3.289000 60.40500 ymin,ymax (A): -18.55700 44.40500 zmin,zma (A): -5.537000 59.11500 x,y,z range (A): 63.69400 62.96200 64.65200 scale (grids/A): 1.651921 object centre (A): 28.55800 12.92400 26.78900 number of atom coordinates read : 3759 total number of charged atoms : 3605 net assigned charge : -8.093967 assigned positive charge : 571.5262 centred at (gu) : 87.40029 80.25200 91.46271 assigned negative charge : -579.6228 centred at (gu) : 87.58791 80.20560 91.44187 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 82156 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34338 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 25835 mr = 55750 m= 2820 mr = 17433 m= 74 mr = 1345 m= 0 mr = 5 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 36352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 374 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 27707 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) : 0.5506403 object centre at (A) : 28.55800 12.92400 26.78900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9805099E-03 -3.3091847E-03 midg,1,midg; midg,igrid,midg -2.7373305E-02 -7.0920405E-03 1,midg,midg; igrid,midg,midg -7.5335861E-03 -3.3122666E-02 gauss-seidel spectral radius is 0.9983011 estimated iterations to convergence 193 setup time was (sec) 1.040000 now iterating at: 18:21:54 rms-change max change #iterations 3.950693 149.1756 at 10iterations 1.688184 59.13013 at 20iterations 0.7253329 27.67940 at 30iterations 0.3114105 9.473728 at 40iterations 0.1337081 4.660302 at 50iterations 5.7191260E-02 1.778420 at 60iterations 2.4527615E-02 0.8215079 at 70iterations 1.0555132E-02 0.3630505 at 80iterations 4.5772945E-03 0.1469646 at 90iterations 1.9851278E-03 6.1504364E-02 at 100iterations 8.8078069E-04 2.9242516E-02 at 110iterations 4.0396670E-04 1.3107300E-02 at 120iterations finished qdiffx linear iterations at : 18:22:02 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 4.0396670E-04 1.3107300E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.580000 DelPhi exited at 18:22:03 9.578u 0.287s 0:10.14 97.1% 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 18:22:03 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3759 !!! WARNING: GLM 77 has a net charge of -0.0940 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: 2.477882 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): -3.289000 60.40500 ymin,ymax (A): -18.55700 44.40500 zmin,zma (A): -5.537000 59.11500 x,y,z range (A): 63.69400 62.96200 64.65200 scale (grids/A): 2.477882 object centre (A): 28.55800 12.92400 26.78900 number of atom coordinates read : 3759 total number of charged atoms : 3605 net assigned charge : -8.093967 assigned positive charge : 571.5262 centred at (gu) : 86.10017 75.37746 92.19391 assigned negative charge : -579.6228 centred at (gu) : 86.38176 75.30836 92.16278 start vw surface at 0.1900000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 190722 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34338 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 89202 mr = 136281 m= 25663 mr = 69928 m= 4316 mr = 19076 m= 324 mr = 2710 m= 7 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.830000 number of dielectric boundary points 82138 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 28813 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) : 1.651921 object centre at (A) : 28.55800 12.92400 26.78900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8217009E-03 0.1093852 midg,1,midg; midg,igrid,midg -0.3972418 -9.5938027E-02 1,midg,midg; igrid,midg,midg -0.1354868 -0.6186616 gauss-seidel spectral radius is 0.9991899 estimated iterations to convergence 277 setup time was (sec) 2.170000 now iterating at: 18:22:05 rms-change max change #iterations 10.17670 308.9799 at 10iterations 5.825437 116.3998 at 20iterations 3.332019 66.65977 at 30iterations 1.886961 38.49753 at 40iterations 1.068481 21.66123 at 50iterations 0.6027662 12.01882 at 60iterations 0.3387814 6.615067 at 70iterations 0.1904182 3.498321 at 80iterations 0.1071369 1.989601 at 90iterations 6.0096037E-02 1.108372 at 100iterations 3.3767767E-02 0.6674631 at 110iterations 1.8942647E-02 0.3426399 at 120iterations 1.0613148E-02 0.2096634 at 130iterations 5.9761195E-03 0.1119924 at 140iterations 3.3751582E-03 6.6002369E-02 at 150iterations 1.9105045E-03 4.0147781E-02 at 160iterations 1.0923204E-03 2.1598339E-02 at 170iterations 6.3607394E-04 1.2388229E-02 at 180iterations finished qdiffx linear iterations at : 18:22:19 total time elapsed so far: 16.08000 # loops : 180 mean,max change (kT/e) : 6.3607394E-04 1.2388229E-02 energy calculations done at 16.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.27000 DelPhi exited at 18:22:20 16.268u 0.309s 0:16.86 98.2% 0+0k 0+0io 0pf+0w