The problem with siRNA simulation

User discussions
1

Hey,
I am working on siRNA trying to make it enter a virus.
However, I have faced an error message in the following picture.

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Although I modified T molecules according to the dna.rtp file ,(the message appears again. it is true that I intend to work with Amber force field, other force fields gave a similar error.
I would be grateful if any one will make a kind assistance.
-Sara

2

Hi,

In the implemented amber force field RNA residues are labelled as RU RC RG RA, while DNA residues are labelled as DT DC DT TA.
If you use self-developed version of AMBER force field will check the residues names in rtp files.

Best regards
Alessandra

3

There are a lot of layers to this issue.

  1. Thymine is a DNA base so it should not be in RNA. Are you sure this is real? If it’s a synthetic construct, is the sugar ribose or deoxyribose?
  2. If this DNA-RNA hybrid really is what you want to simulate, pdb2gmx is going to have problems that you will have to navigate. DT (the proper residue name for thymine in the AMBER force fields) is going to be recognized as DNA, not RNA, so you’ll end up with the exact same error. You’ll have to amend residuetypes.dat to add a fake entry for DT as RNA for the topology to be generated.
  3. The AMBER nucleic acid force fields distributed with GROMACS are ancient and you should seek out better parameters. Other implementations are available from unofficial sources but I would emphasize that AMBER94, AMBER99, etc. are unsuitable for modern DNA or RNA simulations.