aa-tRNA residue parameters/ pdb2gmx

GROMACS version:2018.1
GROMACS modification: No

Hi,

I want to simulate an aminoacylated tRNA. I attached a Phenylalanine residue to the 3’ position of adenosine and ran it through paramchem but now I’m running into a wall with pdb2gmx.

I added the residue to the .rtp file and the residuetypes.dat as RNA.

pdb2gmx breaks the aminoacylated residue into its own chain separate from the rest of the tRNA chain. I did edit the pdb so that all residues have the same chain id.

I also get the error:
“atom N not found in buiding block 1GUA while combining tdb and rtp”

I also see:
Start terminus GUA-1: NH3+
End terminus CYT-75: COO-

It seems like my RNA is being treated as protein? Should it be pulling the [5TER] from the merged.n.tdb instead of the [NH3+]

Does anyone know of any available aminoacylated nucleotide parameters instead or how I should go about setting this up?

Sorry for the broad question.

Thank you!

Dan

Hi,

Have you modified an already implemented force field or did you generate a new one?

For the termini problem, try to use the option -ter (that allow you to chosen the end type).

For modified nucleotides, both AMBER or CHARMM force field have parameters for modified NA, and both this force field have port for GROMACS. Check with force field version are suitable for your case (if any).

Best regards
Alessandra

Hi Allesandra!

I added this aminoacylated nucleotide to Charmm 36.

Thank you for the -ter pointer! Also the -merge option got the chains resolved however it’s having a problem with a “dangling bond” on my modified nucleotide.

I looked through quite a bit of material but can’t find any available aminoacylated adenosines.

Thank you!

Dan

Hi,
you can look at the supplementary material of Xu et al.
doi: 10.1002/jcc.24307. The paper is on RNA modification and CHARMM force field. The supplementary material reports a wider collection of modification than the main text. Maybe there is some modification similar to what you look for.
Best regards
Alessandra

Thank you, Alessandra!