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

[Nash, Anthony]

Agreed! I have had some success using umbrella sampling, but the reaction
coordinate is quite tricky and prone to periodic boundary artefacts. I’m
putting together a script to strip out the force entries where the
corresponding frame demonstrates the long fibril protein seeing itself in
addition to its neighbour. Increasing the box, although possible, size
would make the system extremely expensive to run.

Thanks again
Anthony  



On 10/06/2016 11:25, "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,
>
>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=8d8a4955-7
>>ce
>> 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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