[gmx-users] how to get Eigenvectors

[Tsjerk Wassenaar]

Hi Nahren,

You can try the .g96 format for this, which has high precision. To
understand the format, convert something to .g96 and replace the
coordinates with the eigenvectors.

Hope it helps,

Tsjerk


On Fri, Nov 1, 2013 at 4:10 AM, nahren manuel <meetnahren at yahoo.com> wrote:

> Dear GMX Users,
>
> I performed an ANM calculation at
> http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi
>
>
> It returned me eigenvectors  in the following format (where the second and
> third column represent first and second eigenvector)
>
> 1  0.010551 -0.048553
> 1 -0.022038 -0.042918
>
> 1  0.107906  0.045009
>
> 2  0.007908 -0.061543
>
> 2 -0.002990 -0.054203
>
> 2  0.109087  0.062326
>
> .
> .
> I tried to convert them into trr file, so that I can use them for analysis
> and this is where I am stuck. I converted them to PDB and I loose out on
> the precision of coordinates.
> ATOM      1  CA  LYS A   1       0.011  -0.022   0.108  1.00 10.00
>   C
> ATOM      2  CA  ILE A   2       0.008  -0.003   0.109  1.00 10.00
>   C
> ATOM      3  CA  GLU A   3       0.008   0.011   0.077  1.00 10.00
>   C
>
> I added the reference structure (the structure I submitted to the server
> as frame 1, time 0) to the above PDB file and used g_nmtraj to get the
> projection. Is there a better way to get the eigenvec.trr.
>
> The server also returns Hessian, so can I use this information to get the
> eigenvec.trr using g_nmeig, but I am not sure how the format of nm.mtx
> should be. Can someone advice me on how to proceed further.
>
> Sincerely,
> nahren
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.