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 <[email protected]> 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, "[email protected] on > behalf of [email protected]" > <[email protected] on behalf of > [email protected]> 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 [email protected]. > >> > > > > -- > 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 [email protected]. -- 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 [email protected].
