[gmx-users] editconf- pdb to gro format

[Justin Lemkul]

On 4/1/13 7:22 PM, Juliette N. wrote:
> Hi all,
>
> I am trying to produce gro file from PDB file using editconf.
>
> Here is the pdb file
>
> HETATM    1  C                   0.672  -0.000
> 0.000                       C
> HETATM    2  C                  -0.672  -0.000
> 0.000                       C
> HETATM    3  H                   1.238  -0.928
> 0.000                       H
> HETATM    4  H                   1.238   0.928
> 0.000                       H
> HETATM    5  H                  -1.238  -0.928
> 0.000                       H
> HETATM    6  H                  -1.238   0.928
> 0.000                       H
>
> Then I use: editconf -f X.pdb -o X.gro
>
> But the go file seems no to be correct
>
>      6
>      0         C    1   0.067  -0.000   0.000
>      0         C    2  -0.067  -0.000   0.000
>      0         H    3   0.124  -0.093   0.000
>      0         H    4   0.124   0.093   0.000
>      0         H    5  -0.124  -0.093   0.000
>      0         H    6  -0.124   0.093   0.000
>     0.00000   0.00000   0.00000
>
> Can anyone please help why this is happening?
>

And what exactly is wrong with it?  You have no residue numbers or names in the 
input .pdb file, so none appear in the .gro file.  The coordinates have been 
correctly transformed from Angstrom to nm within the limit of precision.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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