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

[Justin Lemkul]

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

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

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