[gmx-users] minor edits to a .gro file

[jkrieger at mrc-lmb.cam.ac.uk]

Plumed has a dumpatoms command (see
http://plumed.github.io/doc-v2.1/user-doc/html/_d_u_m_p_a_t_o_m_s.html ).
You can create virtual atoms whose position is defined based on existing
atoms or groups thereof. Plumed can be used as a stand-alone driver or
patched onto gromacs for on-the-fly analysis and biasing.

Best wishes
James

> Hi all,
>
> I¹m looking to open a .gro file, add in six hydrogen dummy atoms (I can
> rename the atom name/type, I just need the correct x, y and z coords) to
> the end of an amino acid sidechain and save whilst preserving as much of
> the .gro format as it can.
>
>
> I would normally load the crystal/derived structure as a .pdb into
> Avogadro or smaller fragments from Gaussian output. Unfortunately, as I
> have defined a completely bespoke post-translation amino acid I can¹t
> restore to .pdb with the aim of using Avogadro, too much can go wrong.
>
>
> Recommendations for Gromacs friendly editing tools would be appreciated.
>
> Thanks
> Anthony
>
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