[gmx-users] Editconf - creating .gro file from .pdb file

[Fernando Mattio]

Dear gromacs users,
I used the command editconf -f input.pdb -o output.gro to create the
structure file. Comparing my pdb file and my gro file, they are very
similar, I mean, the gro file is quite allright, because the coordenates are
the same of the pdb file.

But I have the following doubts... please first take a look on my short gro
file generated with editconf.

24
1BLGL C5 1 0.334 0.177 -0.798
1BLGL O 2 0.470 0.168 -0.846
1BLGL C1 3 0.523 0.034 -0.868
1BLGL O1 4 0.653 0.044 -0.915
1BLGL C2 5 0.435 -0.041 -0.970
1BLGL O2 6 0.478 -0.175 -0.982
1BLGL C3 7 0.285 -0.037 -0.929
1BLGL O3 8 0.206 -0.093 -1.031
1BLGL C4 9 0.237 0.106 -0.898
1BLGL O4 10 0.106 0.101 -0.845
1BLGL C6 11 0.302 0.328 -0.777
1BLGL O6 12 0.178 0.346 -0.711
1BLGL H5 13 0.327 0.127 -0.700
1BLGL H1 14 0.523 -0.021 -0.772
1BLGL HO1 15 0.651 0.093 -0.999
1BLGL H2 16 0.445 0.008 -1.069
1BLGL HO2 17 0.421 -0.218 -1.048
1BLGL H3 18 0.273 -0.099 -0.838
1BLGL HO3 19 0.114 -0.091 -1.000
1BLGL H4 20 0.234 0.164 -0.992
1BLGL HO4 21 0.078 0.193 -0.829
1BLGL H61 22 0.380 0.373 -0.715
1BLGL H62 23 0.301 0.381 -0.872
1BLGL H6 24 0.165 0.440 -0.701
0.00000 0.00000 0.00000

What are the three last numbers ( 0.00000 0.00000 0.00000 )??? What do they
mean? Because I compared this file with some others generated with the
pdb2gmx command, and in these cases the three last numbers are all different
from zero! So I really don´t know if my generated gro file is right.
Thank you very much in advance,
Fernando Mattio
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20051013/63a04cf7/attachment.html>