Question about entry not found in rtp file

User discussions
1

GROMACS version: version 2022.2-conda_forge
GROMACS modification: No

Dear community,
I am trying to prepare a protein DNA complex with pdb2gmx (forcefields: AMBER99SB-ILDN protein, nucleic AMBER94) but failing with the fatal error:

Atom P in residue DA 734 was not found in rtp entry DA5 with 30 atoms
while sorting atoms.

However, the dna.rtp file contains a proper DA entry with an entry for atom type “P”. Why is pdb2gmx is checking in entry DA5 instead of DA?

2

It is detecting this particular DA residue to be the 5’-terminus of a chain, hence it is applying DA5.

3

OK, this makes sense. Thanks for your fast reply.