How about that. Structure is ok in vmd. So I guess it is Chimera specific
On Fri, Aug 21, 2015 at 1:18 AM, 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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>
>
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Received on Thu Aug 20 2015 - 18:00:03 PDT
