Atom H1 in residue ACE 1 was not found in rtp entry

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1

GROMACS version:
GROMACS modification: Yes/No
Hello, everyone

I’m trying to generate a .gro and .top files from the .pdb structure of polyglycinealanine, using the Amber99 FF. When trying to do so, however, the following error appears:
Atom H1 in residue ACE 1 was not found in rtp entry ACE with 6 atoms
while sorting atoms.
H1 atom is included in the aminoacids.rtp file witht the correct name, and -ignh option doesn’t work either.
What should I do?

2

What are you choosing as termini when prompted by pdb2gmx? When reporting problems with pdb2gmx, please always copy and paste the entire screen output and provide it for diagnostic purposes. The complaint about H1 suggests you are using normal N-terminal patching, which is incorrect for a capped polypeptide sequence (for which you need to choose “None” as the terminus type).