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

Sampo Karkola sampo.karkola at helsinki.fi
Mon Oct 15 09:51:10 CEST 2007


problem solved and it was a stupid mistake by me. The reference 
structure I used (the -s option in trjconv) had the ligand out of the 
active site. When I selected another reference with proper positioning 
of the system, everything went well. Thanks anyway!


Check out these cool words by Mark Abraham:
> 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.
> Mark
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