[gmx-users] dihedral angles

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 28 01:07:53 CEST 2011

Sai Pooja wrote:
> Hi,
> I am running a simulation for capped alanine dipeptide and I now need to 
> extract the dihedral angles. However, one of the nitrogen is named NT 
> instead of NH due to which g_rama is not able to give the dihedral 
> angles. Is there any other program I can use to get dihedral angles? I 
> tried g_dih and g_sgangle but didnt get what I wanted. For g_sgangles I 
> specified 2 groups with 2 atoms each and used -oa. The .xvg file 
> contains 3 columns instead of 2 and there are 2 values against time... I 
> am not sure what that means
> The other alternative is to simply run the simulation again by changing 
> the NT to N (and NHT to NH) in the gro and top files which would be a 
> waste of time.

You should just be able to re-name these atoms in your topology, create a new 
.tpr file, and re-run your analysis, not the simulation.  There are no atom 
names in the trajectory file, it's all based on what's found in the topology.


> KIndly let me know if there is an easy way out.
> Pooja
> -- 
> Quaerendo Invenietis-Seek and you shall discover.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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