Thanks, I will look into the paper.
Soma
> Although I haven't had a chance to use PCA in AMBER yet, I have used Bio3D
> to make a movie from PCA motion that can be viewed in VMD.
> If you want to qualify domain motion, you could try using Local Feature
> Analysis. I remember reading an interesting paper on applying the
> technique to biomolecules by Zhang and Wriggers in Proteins, 2006.
>
>> Dear AMBER Users,
>>
>> I am trying to study domain motions in my protein using PCA analysis of
>> the
>> ptraj module. I have successfully performed PCA and have got the
>> projection
>> files.
>>
>> The next problem is to visualize the motions and generate porcupine plots.
>> For
>> this, I installed ied-2.02 as a plugin in VMD 1.8.6. The plugin seems to
>> work
>> fine with gromacs examples but fails to work with AMBER format files. I
>> checked
>> online and it says that ied can only use formats generated using ptraj8.
>> Is this
>> true?? Also i am not able to draw the arrows using this plugin , which
>> seems to
>> be a bug with vmd 1.8.6.
>>
>> I can use PCASuite, however my CRD files are in the .gz format and
>> PCASuite is
>> not able to read the gunzipped files. Also, I have a set of 20 CRD files
>> and I
>> want PCASuite to read all the CRD files one after another, how can this be
>> done???? Is there a way of scripting PCASuite, wherein one can use trajin
>> command and PCAsuite in combination ??
>>
>> Finally, can some one take me through the process of generating poocupine
>> plots
>> from the PCA analysis done using ptraj of AMBER 9. Also, is there a way of
>> quantifying domain motions. Is it ok if i calculate the angles between
>> two set
>> of residues from the centre of the domains ???
>>
>> Thanks,
>> Soma
>>
>>
>>
>>
>>
>>
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Received on Sat Sep 21 2013 - 05:30:03 PDT
