Working with Thioester bond

[Aravind Ravichandran]

Hi Everyone,
I would like to perform NMA on a system of interest which contains a thioester bond (CONNECT records are present in the PDB) linking two proteins. When I load the PDB in bio3d, perform analysis and write output PDB again, the produced PDB does not contain thioester bond.
I also tried using amber topology and coordinate files (with thioester bond) instead of a PDB file and ended up with the same problem.
How would I go about this problem? Can anyone help me with this?
Regards,
Aravind R

[Xinqiu Yao]

Currently bio3d does not support 'CONNECT' records. If you are using bio3d to do elastic network model based NMA, it should not matter because in ENM atoms are linked by checking distance (so, if the two residues are close enough, they will be linked no matter there is a covalent bond or not).

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If you are using bio3d for some pre-processing purpose, you may need to add the missing record manually or consider using other software to do the task.

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Hope it may help.

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[Aravind Ravichandran]

Xinqiu Yao, thanks for the reply.

How do I manually add a bond between 2 atoms?

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[Xinqiu Yao]

It depends on what ENM force field you used. Some force fields (such as 'ANM') support a distance cutoff and so by just increasing the cutoff value you should be able to include more pairs. Unfortunately, there is no automatic way to add a specific bond unless you provide your own potential energy function through the pfc.fun argument of the nma() function.