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

[David van der Spoel]

On Thu, 2005-10-13 at 11:20 +0200, Fernando Mattio wrote:
> 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.
it's the box.

check chapter 5 in the manual and run the programs editconf and or
genbox with the -h flag
> Thank you very much in advance,
> Fernando Mattio
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++