[gmx-users] g_anaeig error inconsistent shifts

[Tsjerk Wassenaar]

Hi Tasneem,

So your tpr file doesn't match your trajectory. How come, or why is that?
And if your eigenvectors correspond to main chain atoms you can't use
protein for analysis.

Hope it helps,

Tsjerk
On Mar 12, 2015 6:07 AM, "tasneem kausar" <tasneemkausar12 at gmail.com> wrote:

> for PCA i used the g_covar followed by g_anaeig.
> i used the command line for g_covr as
> g_covar -f full.xtc -s full.tpr -o eig.xvg
> I have selected the protein for least square fit and main chain for
> covarience analysis.
> There is a warning message.
> WARNING: number of atoms in tpx (312) and trajectory (1061) do not match
>
> The above command generates the files average.pdb, eigenvec.trr and eig.xvg
> Then, i am using the eigenvec.trr file and averagr.pdb file for g_anaeig
> The commnan line for g_anaeig is given below.
> g_anaeig -f eigenvec.trr -s full.tpr -od 2dproj.xvg
> For least square fit i have selected the protein and same for the
> eigenvectors
> This gave the following message;
> There were 40 inconsistent shifts. Check your topology
> where is the problem occured?
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