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

[Nash, Anthony]

James and Justin,

Thanks for your suggestions. This was ultimately to hack around with the
PMX toolkit for making dummy atoms in preparation for free energy
calculations. Unfortunately, I’m back to the drawing board (likely to be
umbrella sampling) as an alchemical morphing of a glycated cross linked
amino acid pair into two separate amino acids might work, but the verse
reaction will cause all manner of constraint issues with gromacs (bond
formation over a potential out of range distance).

Thanks again
Anthony


Dr Anthony Nash
Department of Chemistry
University College London





On 09/06/2016 23:52, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of jkrieger at mrc-lmb.cam.ac.uk"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
jkrieger at mrc-lmb.cam.ac.uk> wrote:

>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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>