Hi, The flexibility of the ligand due to its internal motions is a big issue when I turn off protein-ligand interactions in the decoupled state (state 1). Applying Boresch's restraints between the protein and ligand, applying positional retraints on all the atoms of the ligand or adding dihedral restraints is not sufficient to get the rigidified ligand in the case that the ligand is very flexible. So, if the ligand were quite rigid, the target system (state 1) would be sufficiently similar to the reference system (state 0). For instance, the intersection of the work distributions of the forward (0-->1) and backward (1-->0) state would provide the accurate estimates of free energy... If GROMACS have the ability to constraint all the internal coordinates of the ligand, then the cost of the angle, bond and dihedral constraints can be calculated with an extra step. That is easy.
Do you have any plans for the implementation of such a feature to the next version of GROMACS-2018.1? :) On 9 May 2018 at 11:36, Mark Abraham <[email protected]> wrote: > Hi, > > Of what would that be a good physical model? > > Mark > > On Wed, May 9, 2018, 10:07 Ahmet Yildirim <[email protected]> wrote: > > > Hi, > > > > With stiff restraints using standard GROMACS versions I couldn't get what > > I want. If Developers implement some like this: > > contraints-grps = ligand > > constrains = all-bonds all-angles all-dihedrals > > > > it would be wonderful :) > > > > > On 9 May 2018, at 10:56, Felipe Merino < > > [email protected]> wrote: > > > > > > Hi, > > > > > > I guess you can always get a similar final result using some stiff > > restraints with gromacs/plumed. > > > > > > Best > > > > > > Felipe > > > > > > > > >> On 09/05/18 09:48, Ahmet Yildirim wrote: > > >> Hi, > > >> > > >> I am facing with the same problem... Unfortunately GROMACS does not > have > > >> the capability to constraint all the internal coordinates (bond > lengths, > > >> bond angles and dihedral angles) of a certain group (e.g. ligand) in > the > > >> simulation system. Hope that Developers will take into consideration > the > > >> implementation of such a feature to the next version :) > > >> > > >> > > >> > > >>> On 8 May 2018 at 14:23, Mark Abraham <[email protected]> > wrote: > > >>> > > >>> Hi, > > >>> > > >>> There is no general support for rigid body dynamics in GROMACS. > > >>> > > >>> Mark > > >>> > > >>>> On Tue, May 8, 2018, 12:52 Qasim Pars <[email protected]> wrote: > > >>>> > > >>>> Dear users, > > >>>> > > >>>> I would like to constraint all the angles and dihedrals of a ligand > to > > >>>> make it rigid but Gromacs does not have this capability for the > > >>> dihedrals. > > >>>> However, the angle and dihedral restraints do not make it rigid as I > > >>> want, > > >>>> as it is very flexible. > > >>>> > > >>>> Do you have an idea on how I can make the ligand rigid using > gromacs? > > >>>> > > >>>> Thanks in advance, > > >>>> -- > > >>>> 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]. > > >>> > > >> > > >> > > > > > > -- > > > Felipe Merino, > > > Max Planck Institute for Molecular Physiology > > > Department of Structural Biochemistry > > > Otto-Hahn-Str. 11 > > > 44227 Dortmund > > > Phone: +49 231 133 2307 > > > > > > ORCID: https://orcid.org/0000-0003-4166-8747 > > > Publons: https://publons.com/a/1305699/ > > > Researchgate: https://www.researchgate.net/profile/Felipe_Merino > > > > > > -- > > > 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]. > -- Ahmet Yildirim -- 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].
