mass weighting could not be grouped by residues

[Former user]

I performed All-atom normal mode analysis for a pdb structure (aanma.pdb) in order to calculate residue-wise fluctuations. The NMA was successful and I obtained the fluctuations but I got the following Warning message:

In aanma.pdb(kin_pdb, keep = 17, outmodes = "calpha") : mass weighting could not be grouped by residues

Because of this, I was not able to map the fluctuations to their corresponding residue numbers. I had performed the same analysis to several similar structures and never had this problem. Can someone point out what's happening here? I am also attaching the PDB file which was given as input.

sessionInfo() output:

R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.6 LTS

other attached packages: [1] bio3d_2.3-4.9000

[Xinqiu Yao]

Hi,

‌

That is most likely your pdb file contains ligands, which will be included in the NMA calculation but cannot be output because of the lack of C-alpha atom. Strip ligand molecules and try again. It should solve the problem.

[Xinqiu Yao]

No response from the user.