[gmx-users] dihedral angles

Sai Pooja saipooja at gmail.com
Mon Mar 28 01:06:07 CEST 2011


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

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

KIndly let me know if there is an easy way out.


Quaerendo Invenietis-Seek and you shall discover.
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