Can't read a non-proteinogenic amino acid

[Roxana Maria]

Hello,

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I have a few simulations that contain a 3-letter coded non-proteinogenic amino acid.

I read the pdb file and printed its sequence with:

pdbseq(pdb,  aa1 = FALSE)

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However, this amino acid is not printed. I would like to ask if this is a problem of the pdbseq or if this amino acid is skipped from reading and from the future analysis (RMSF and PCA).

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Also, when I use print(pdb) it does find it here but its not shown in the sequence:

Protein Atoms#: 7242 (residues/Calpha atoms#: 445)
Nucleic acid Atoms#: 0 (residues/phosphate atoms#: 0)

Non-protein/nucleic Atoms#: 13 (residues: 1)
Non-protein/nucleic resid values: [ AIB (1) ]

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I tried the same thing with a pdb from RCSB that has these types of amino acids and it read and showed those residues.

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If anyone can help me with an explanation or suggestion I would very much appreciate it. Thank you.

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[Xinqiu Yao]

The residue was recognized as a “ligand”. So, yes, it will be skipped in analyses that focus on protein residues and in the output of pdbseq().

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One quick way to solve it is to modify the topology (usually a single PDB file) to make it recognizable. For example, you can change the residue name to some standard amino acid and the atom name equivalent to C-alpha to “CA” (if necessary).

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Double check once you done the modification by read.pdb() and printing it in R.

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It won’t change results because most analyses just care about XYZ coordinates. What you need is just to remember where the residue is located (by residue number, for example).

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