[gmx-users] Question about the No chi1 & chi2 angle problem with gmx Chi

Xingcheng Lin linxingcheng50311 at gmail.com
Sat Aug 19 19:22:24 CEST 2017


I am using Gromacs function gmx chi to calculate the X1 and X2 angle based
on my pdbs. However, it prompts this warnning:

WARNING: not all dihedrals found in topology (only 317 out of 496)!
No chi1 & chi2 angle for VAL7
No chi1 & chi2 angle for ALA13

However, the output seems to be complete for these indicated residues
where, for example, ramaPhiPsiVAL7.xvg has all X1 and X2 dihedrals I wanted.

I am wondering if this is a redundant output from gmx Chi or is it
something I need to pay attention to?

I am using Gromacs 5.0 for calculation. The command is:

gmx chi -s pdbFile -f xtcFile -rama -xvg none


P.S. I saw a similar issue online at

However, it doesn't seem to have a conclusion yet.

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