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

[Nash, Anthony]

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


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
>> >>
>> >> --
>> >> Gromacs Users mailing list
>> >>
>> >> * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >> posting!
>> >>
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
>> >> * For (un)subscribe requests visit
>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> >>send
>> >> a mail to gmx-users-request at gromacs.org.
>> >>
>> >
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at
>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>send a mail to gmx-users-request at gromacs.org.