Hello everyone, I am currently working on miRNA- mRNA interaction study. Further, I would like to do MD simulations for the miRNA-mRNA models.
For the Simulation, I have modelled this complex using the Alphafold server. But when I try to use AlphaFold models for the Gromacs MD simulations, it gives some error when I apply the force field (Amber - 2010).
The error is "Atom OP3 in residue U 1 was not found in rtp entry RU5 with 28 atoms while sorting atoms."
If I change the atom name, it shows another atom is missing (attached the screen shot with this Q&A)
Is there any updated force field or modelling algorithm?
Kindly help me to solve this issue.
Hello Ravichandran Subramaniam,
It is a general problem when using AlphaFold to model RNA or DNA structures. Generally, the structure of the first residue of RNA or DNA must be free of the phosphate group. So, you should delete the first four atoms of the RNA chain, which include OP3, P, OP1, and OP2. These atoms are not included in the forcefield, causing an error. The structure should start with the atom O5'.
Hello Nopawit Khamto ,
I removed all the OP3, P, OP1, and OP2 atoms from the file. Now, The Amber force field is working for the model. Thank you for the suggestion.