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 DA1 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.
Thank you for your time and assistance.
Best regards,
fatemeh,
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Received on Sat Sep 30 2023 - 02:30:02 PDT
