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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Aug 20 2015 - 17:30:05 PDT
