Thanks Jason! Will post your suggestion to the chimera list
On Fri, Aug 21, 2015 at 2:36 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> What is happening here is that Chimera's topology file parser is trying to
> guess what the element of each atom is. Atom name is unreliable (every
> carbon-alpha is named "CA", which makes it hard to distinguish between
> calcium and carbon, for instance), as is atom type. Chimera tries to use
> that information, but not very hard (i.e., if the atom type is not the same
> name as the element, it tries the masses) -- I checked the source code to
> figure out what was happening.
>
> Typically, the most reliable way to determine the atomic number, by far, is
> using the atomic mass (unless of course the atomic number is available
> directly). So when you repartition the masses, Chimera starts assigning
> the wrong elements to most of the atoms. This is why using the original
> prmtop file works, but the repartitioned masses one does not.
>
> The prmtop only recently started storing the atomic numbers directly, and
> the Chimera parser has not been updated for that change. For Chimera
> developers, that is the easiest fix.
>
> All the best,
> Jason
>
> On Thu, Aug 20, 2015 at 9:03 PM, George Green <soyo.green.gmail.com>
> wrote:
>
> > Thanks Adrian & Hai,
> >
> > So I guess if i just use the original (nornmal 2fs) topology file for all
> > cpptraj, vmd and chimera analysis, there should be no problems.
> >
> > Glad the solution was that simple. Was anticipating a bit of a nightmare.
> >
> > Many thanks!
> >
> > On Fri, Aug 21, 2015 at 1:32 AM, Nhai <nhai.qn.gmail.com> wrote:
> >
> > > I think HMR topology affects the analysis requiring mass, like center
> of
> > > mass. So it's better to use original top (which is easy to generate).
> > >
> > > Hai
> > >
> > > > On Aug 20, 2015, at 8:18 PM, George Green <soyo.green.gmail.com>
> > wrote:
> > > >
> > > > yup, thought it would go that way. though, i was wondering whether
> this
> > > is
> > > > going to affect the analytical tools offered in 3rd party programs
> such
> > > as
> > > > chimera, pymol and vmd. This might make analysis complicated! Surely
> > > > someone else must have had to deal with this issue?
> > > >
> > > >> On Fri, Aug 21, 2015 at 1:15 AM, Adrian Roitberg <roitberg.ufl.edu>
> > > wrote:
> > > >>
> > > >> So, if you load the SAME coordinate file with the regular topology
> it
> > > >> looks ok ?
> > > >>
> > > >> My only possible guess would be that chimera decided about
> distances,
> > > >> etc based on the atomic mass and NOT on the atom type. If that is
> the
> > > >> case, there is nothing you can do, except tell the chimera
> developers
> > to
> > > >> change that.
> > > >>
> > > >> adrian
> > > >>
> > > >>
> > > >>> On 8/20/15 7:49 PM, George Green wrote:
> > > >>> Hi,
> > > >>>
> > > >>> I set up up simulations to use hydrogen mass repartitioning and ran
> > > some
> > > >>> simulations with no apparent problems. However, on visualising with
> > > >>> chimera, the protein does not show ribbons which makes
> visualisation
> > > >>> difficult. Please see attached figure.
> > > >>>
> > > >>> The problem only occurs with the topology file created after
> feeding
> > > into
> > > >>> parmed to change masses. I guess the problem is due to atoms being
> > > >> further
> > > >>> apart than the defined distances in chimera? It would be good if
> > > somebody
> > > >>> could confirm that this is a known issue and not the result of
> > > incorrect
> > > >>> parametrisation? Also, if it is expected behaviour, is there any
> way
> > to
> > > >> get
> > > >>> ribbon style visualisation back?
> > > >>>
> > > >>> many thanks
> > > >>>
> > > >>>
> > > >>> _______________________________________________
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> > > >>
> > > >> --
> > > >> Dr. Adrian E. Roitberg
> > > >> Professor.
> > > >> Department of Chemistry
> > > >> University of Florida
> > > >> roitberg.ufl.edu
> > > >> 352-392-6972
> > > >>
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>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Aug 21 2015 - 07:00:06 PDT
