nma_for_large_macromolecular_complex

Issue #503 resolved
karolk
created an issue

Hi All,

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.

thanks karl

Comments (7)

  1. Xin-Qiu Yao

    I think this is just a warning that some regions might have large fluctuations because of the "chain broken" (due to long CA-CA distance; such as between chains or within one chain but around unresolved residues). It shouldn't matter for the final results.

    Regarding covalent bond between chains, it shouldn't happen in bio3d. But I am not quite sure. Lars, any comments?

  2. Barry Grant

    The msg is just letting you know that there are chain breaks in your system as sometimes users don't realize this before hand. You are fine to keep on going here if you understand this.

  3. karolk reporter

    Hi,

    Thank you for your answers.

    Yes. They are "chain brakes" within a few subunits due to the presence of the unresolved regions.

    I will remove these subunits and repeat calculations in order to see whether the problem is really about these subunits.

    I will let you know.

    thanks

  4. karolk reporter

    Hi,

    I checked. The same warning message appears after removing incomplete subunits from the calculations. So, as Barry said, it looks that it is only an info message.

    However, to stay on a safe side, can you please confirm that:

    1. nma() does not introduce covalent bonds between the different chains?

    2. nma() does not introduce covalent bonds within a chain, that is, between the chain brakes?

    thank you

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