Can't find a force field that will accept my .pdb file

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1

GROMACS version: 2018

Hi everybody. I’m very much a beginner with GROMACS and MD software in general, but I’m interested in using it to model some self-assembled monolayers for my research. In any case, after assembling my desired system in Avogadro, I converted it to a .pdb file and then put it into pdb2gmx only to find that when I selected my desired force field it threw me a “Residue ‘UND’ not found in residue topology database” error.

I looked this error up in the GROMACS 2018 documentation, and although I now have somewhat of an idea of why this happened, I’m not entirely sure how to fix it. I find this even more puzzling because my initial system and choice of force field (AMBER99SB-ILDN) is pretty much identical to the paper I’m basing my procedure off of, and it appears to have worked for them. I’m not entirely sure what I did wrong here.

Any help on this matter would be greatly appreciated.

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pdb2gmx can only generate topologies for residues it knows, which are all found in the .rtp file(s) for your force field. If your species is not there, you’ll have to add it: http://manual.gromacs.org/current/how-to/topology.html#adding-a-new-residue

If someone has already done simulations with this non-standard residue, save yourself some effort and ask them to provide the corresponding force field files.