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.
-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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