I want to perform NMA of a large macromolecular complex, composed of several chains, but I am getting the following message "Warning message: In nma.pdb(PDB, ff = "calpha", keep = 16, mass = TRUE) : Possible multi-chain structure or missing in-structure residue(s) present Fluctuations at neighboring positions may be affected." .
I tried to diagnose and decompose the problem:
I renumbered a whole protein from 1 and I left original chain labels
I renumbered each chain from 1 and I left original chain labels
I assigned a single chain label to a whole complex and protein was renumbered from 1
None of these worked. So, I assume that it is not about presence of different chain labels, nonconsecutive numbering, presence of hetatms ( I rm these) etc. My first question is: how nma() determines where the chain starts and where it ends? In the last of the listed examples, the complex is represented as a single chain with residue numbering starting from 1. The nma() should treat as a single chain. I tried everything. I have no idea how I should feed the function in a way it will take a protein as a single chain or complex composed of individual chains.
Second, I assume that nma() "should know" exactly where the chain starts and ends?Otherwise a topology of a system will be incorrect. I mean, the code might introduce (I don't know, I just speculate) the artificial interatomic connections between the chains, which do not exist. None of the subunits is covalently bonded to each other.
Summarising, is there any way to perform NMA of a multi chain complex?
I use the newest version of bio3d.