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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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> --
>> 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 - 18:00:04 PDT
