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

[Mark Abraham]

Hi,

One generally uses distance restraints to limit the sampling space of the
separated amino acids, but exactly how to implement that might take a bit
of iterating. GROMACS 5.1 can do inter-moleculetype restraints, but that
probably isn't necessary/useful in this context.

Mark

On Fri, Jun 10, 2016 at 11:32 AM Nash, Anthony <a.nash at ucl.ac.uk> wrote:

> 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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