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

Justin Lemkul jalemkul at vt.edu
Sun Aug 20 00:15:33 CEST 2017

On 8/19/17 1:21 PM, Xingcheng Lin wrote:
> Hi,
> 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?

It's reminding you of basic amino acid structure.  Valine has chi1 but not chi2, 
alanine has neither, etc.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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Blacksburg, VA 24061

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