Aligned to what? RMSD allows you to align to a given set of coords.
Bill
On 7/24/17 5:56 PM, Elisa Pieri wrote:
> Sorry, maybe I didn't make my question very understandable :)
> I would like to get a new nc file where the protein is aligned in each
> frame as an output. Can RMSD do this? From the manual,it doesn't seem so.
>
> Elisa
>
> On Mon, Jul 24, 2017 at 11:09 PM, Xing <stecue.gmail.com> wrote:
>
>> Dear Elisa,
>>
>> Sorry if I misunderstand the question...I don't know the details of REMD,
>> but why couldn't we just use the "rmsd" command in cpptraj? It has a
>> "previous" option to align current frame to its previous
>> frame, or whatever frame if using "ref #" according to the manual.
>>
>> Thanks and best wishes,
>> Xing
>>
>> On 07/24/2017 03:59 PM, Elisa Pieri wrote:
>>> Hello,
>>>
>>> I have a curiosity: I have a nc trajectory obtained from REMD, so the
>>> frames are actually not-consecutive snapshots. Is there a tool to align
>> the
>>> protein from frame to frame?
>>>
>>> I'm performing cluster analysis on it, and would like to be sure that
>> this
>>> issue is not a problem in calculating RMS and average structures. Right
>>> now, average structures are completely unrealistic.
>>>
>>> Suggestions?
>>>
>>> Elisa
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>>
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Received on Mon Jul 24 2017 - 15:30:02 PDT
