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