Re: [AMBER] hydrogen mass repartitioning visualization in chimera

From: Adrian Roitberg <>
Date: Thu, 20 Aug 2015 20:15:04 -0400

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.


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
> _______________________________________________
> AMBER mailing list

Dr. Adrian E. Roitberg
Department of Chemistry
University of Florida
AMBER mailing list
Received on Thu Aug 20 2015 - 17:30:03 PDT
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