[gmx-users] non-existent angles found from trajectory g_angle

Mark Abraham Mark.Abraham at anu.edu.au
Fri Oct 12 15:52:07 CEST 2007

Sampo Karkola wrote:
> Hi Mark,
> visualisation of the .trr file with vmd succeeded, but the original 
> problem remains.The -pbc cluster option did not do any better. The weird 
> thing is that after trjconv with -pbc cluster, -center tric and -ur 
> compact (or without the latter two) produces a trajectory with the 
> ligand in the correct position but some of the surface atoms of the 
> protein jump between the boxes. If I then do trjconv with -fit 
> progressive (or rot+trans) the protein is displayed as a whole but the 
> ligand jumps out of the box. I've used the protein_heme_ligand group in 
> the index file as the centering, clustering and fitting group.
> And in all cases I see the weird angles at 50 deg, which are not shown 
> in vmd visualising the system with ligand staying in the cavity.

Well, find out what frames have these occurring and see why it is.


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