[gmx-users] Re: Trajectory and ED - (not old question again)

[Tsjerk Wassenaar]

Hi Kavya,

For us to say anything sensible about it, we should at least know
exactly what you've tried. Copy-paste the commands exactly as you
issued them, and provide the parts of the output that seem relevant.

Cheers,

Tsjerk

On Thu, Jun 23, 2011 at 9:54 AM, Kavyashree M <hmkvsri at gmail.com> wrote:
> Dear Sir,
>
> I tried fitting the proteins of the trajectory in pymol
> as mentioned in your (Dr. Tsjerk's) tutorial, but later
> I tried using the trjconv -fit rot+trans to fit the proteins
> in the trajectory as you had mentioned.
>
> I do not observe this degree of movement in protein
> when I view the trajectory along any 1-5 eigen vectors.
> This trajectory along any of these eigen vector is very minute
> and cannot be compared to that obtained after superposing
> the structure in the trajectory. Why is it so?
> Please let me know if I am understanding the concept wrong.
>
> Thanking you
> With regards
> M. Kavyashree
>
>
> On Thu, Jun 23, 2011 at 11:56 AM, Kavyashree M <hmkvsri at gmail.com> wrote:
>>
>> Thank you Sir!
>>
>> With regards
>> M. Kavyashree
>>
>> On Thu, Jun 23, 2011 at 11:50 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
>> wrote:
>>>
>>> trjconv -fit rot+trans
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>> On Jun 23, 2011 8:12 AM, "Kavyashree M" <hmkvsri at gmail.com> wrote:
>>>
>>> Dear Users,
>>>
>>> Are there any tool for superposing the trajectory
>>> structures form MD. Please correct me if I am asking
>>> any illogical question.
>>> My previous question was regarding the trjconv output
>>> pdb trajectory, is there a way to superpose all these
>>> structures?
>>>
>>> Thank you
>>> With regards
>>> M. Kavyashree
>>>
>>> On Wed, Jun 22, 2011 at 10:52 PM, Kavyashree M <hmkvsri at gmail.com> wrote:
>>> > > Dear users, > >    I...
>>>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands