I am currently working on DNA construction using the 3xDNA web server. I have encountered an issue when attempting to save the constructed DNA as a PDB and subsequently applying the Amber force field using pdb2gmx in Gromacs.
The error message I'm encountering is as follows:
"Atom P in residue DA 1 was not found in rtp entry DA5 with 30 atoms while sorting atoms."
To work around this issue, I have been manually deleting the first phosphate and its attached oxygen atom, which allows me to successfully run pdb2gmx with the Amber force field. However, I am curious if there is an alternative solution to resolve this problem without the need to delete these atoms.
I would greatly appreciate any insights or suggestions you may have on how to address this issue more effectively.
If you are attempting to assemble a topology using pdb2gmx, the atom names are expected to match those found in the rtp file that define the building block(s) in your structure. In most cases, the problem arises from a naming mismatch, so simply re-name the atoms in your coordinate file appropriately. In other cases, you may be supplying a structure that has residues that do not conform to the expectations of the force field, in which case you should investigate why such a difference is occurring and make a decision based on what you find - use a different force field, manually edit the structure, etc.
I got this from the Gromacs manual. It could help you. Also, below is the link to find related errors and solutions on Gromacs Common errors when using GROMACS — GROMACS 2020 documentation
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