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

[Mark Abraham]

Hi,

I certainly haven't tried something as complicated as taking three
fragments, some charged, and morphing them to a neutral structure, but I
would consider very seriously doing it in several stages, e.g. breaking
into neutral fragments, dissociation of fragments, charging of fragments.

Mark

On Fri, Jun 10, 2016 at 12:12 PM Nash, Anthony <a.nash at ucl.ac.uk> wrote:

> Hi Mark,
>
> I had considered (and I still am) defining a distance constraint between
> the lysine-N and arginine-N-N on their sidechains, which defines the
> points where the morphing into a bond formation would be.
>
> I am essentially trying to morph back and forth into this structure:
> http://www.chemspider.com/Chemical-Structure.26333276.html?rid=8d8a4955-7ce
> 4-43db-b30f-12b8b6cc2f64
> <http://www.chemspider.com/Chemical-Structure.26333276.html?rid=8d8a4955-7ce4-43db-b30f-12b8b6cc2f64>
>
>
> Yet, I wondered whether the charges on the lysine and arginine would cause
> a bias to the result as I would be holding them very close. Still thinking
> about this one, I am going back to umbrella sampling for a while.
>
> Cheers
> Anthony
>
>
> Dr Anthony Nash
> Department of Chemistry
> University College London
>
>
>
>
>
> On 10/06/2016 10:37, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
> behalf of Mark Abraham" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> on behalf of mark.j.abraham at gmail.com> wrote:
>
> >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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> >>
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