Running MD with a UNL residue name in the pdb file

User discussions
1

GROMACS version: 2023.5
GROMACS modification: No

Hello,

The residue name is list as UNL. After running the GROMACS command to generate the topology, which fails because UNL is not listed in the residue topology database. Is it possible to manipulate GROMACS to identify the UNL residue name and generate the topology file to proceed towards MD production?

Ryan Molitor

2

I am using the charmm36-jul2022 force-field on a local cluster.

Ryan Molitor

3

If it is a constituent residue in the chain of a biomolecule, you need to parametrize and validate the species, then write an .rtp entry for pdb2gmx to understand how to include it. If it is a noncovalently bound species like a ligand, you still need to parametrize and validate it, but then you can simply #include its topology in the system .top file.

4

Thanks. Is it possible to run GROMACS at high temperatures, like 1000K to 5000K?

ryanm

5

With a sufficiently small time step, yes, but no biomolecular force field has ever been validated at that temperature. I know from toying around at 500 K that peptide bonds will isomerize at that temperature, so you’re bound to get some strange behavior, which may or may not be correct. But you’d be in the wilderness in terms of convincing anyone that the model is valid.

6

I see. Thank you.