Simulating a Reverse Transcriptase complex with RNA, DNA

bhavya_28
Fri, 28 Nov 2025 17:08:14 +0000
User discussions

Hi, I have been trying to simulate a reverse transcriptase (PDB 6AR1) that is in complex with RNA, DNA, DTPs, MG, SO4. Gromacs cribs because it cannot recognise if the Mg, DTP, SO4 is in the same chain as the protein. Any help on this will be appreciated.

Also, a general MD question, how do I know if the parameters I set are right for the kinda of protein I have? And How do I prepare my PDB before running pdb2gmx.

2 posts - 2 participants