[gmx-users] Dihedral angle PCA

[anu chandra]

Hi David,

Thanks for the reply. I have not tried yet. Since I didn’t find query about
the dihedral PCA in the mail list, I thought of confirm about the steps
mentioned in the web site.


Regarding the use of dihedral PCA, the protein with which I am working
behave differently from others. From literature, this protein shows minimal
backbone conformational changes during ligand binding and presumed that
there is high degree of side-chain conformational changes during binding to
ligand. This made me to think about dihedral PCA for get some information
about the ligand binding. What is your opinion in this regard?


Is there any other sort of analyses that can help me to quantify such
side-chain conformational changes and also to locate the regions in
protein, which have  high degree of side-chain conformational changes
during ligand binding?

Waiting for your valuable reply.

Thanks and regards
Anu




On Thu, Apr 11, 2013 at 9:05 PM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

> On 2013-04-10 08:33, anu chandra wrote:
>
>> Dear Gromacs users,
>>
>> I would like to do side-chain dihedral angle PCA for my protein. The
>> protein contains 293 residues. I came across an explanation about dihedral
>> PCA in gromcas website (
>> http://www.gromacs.org/**Documentation/How-tos/**Dihedral_PCA<http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA>).
>> Is it possible
>> to do side-chain dihedral PCA using the same methodology? Is there any
>> other programmes anyone came across for side-chain dihedral PCA?
>>
>>
>> Waiting for your valuable reply.
>>
>> Thanks in advance
>>
>> Regards
>> Anu
>>
>>  Have you tried following the steps there? I think it should work.
>
> Other than that dihedral PCA is regarded as not very useful by at least
> some people because it is difficult to interpret the results in structural
> terms. For instance maxima in a multidimensional torsional energy landscape
> may be due to atoms coming close (hence preventing the sampling) without
> giving any real information on the structures. But this is for you to
> decide :).
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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