Aptamer-Protein Interaction

User discussions
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1

GROMACS version: 2021.4
GROMACS modification: No

All,

Good morning and for you more experienced users, my question may seem trivial. I am trying to look an Aptamer-Protein Interaction. I have gone through the tutorials posted by Dr. Lemkul at GROMACS Tutorials but am running into errors when I try to run my protein and aptamer. Currently, I get an error when I convert the pdb file to gro using the pdb2gmx command where “Warning: No residues in chain starting at NAG1 identified as Protein/RNA/DNA.” What is the best method do dealing with this error?

Please keep in mind I am a beginner with gromacs, but am excited to learn it. With that said, I am open to any thoughts on how to further process the file so I can better understand the interactions between the aptamer and protein. (I would upload the files but can’t seem to add a pdb file for your review.)

Thank you.

2

What ff you are using? You need to change the naming of atoms according to the itp of respective forcefield.

3

This is not an error; it is merely an advisory message. Did pdb2gmx finish successfully, or did it fail (you will get an obvious fatal error in the latter case)?

The note printed by pdb2gmx is to warn users if they have a malformed input coordinate file that may contain a mixture of species (e.g. a protein and ligand). This would prompt editing of the file to remove the nonstandard species or to at least introduce chain separators between them for proper processing.