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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Received on Thu Aug 20 2015 - 18:30:03 PDT
