Creating a topology for DNA

User discussions
1

Hi
I want to create a topology for dna and do molecular dynamics calculations for dna-ligand but I got the following error, can you help me.
Thank you.
residue dc1 not found in residue topology dtabase for more information and tips for trouleshooting, please check thegromacs

2

It means the topology for residue dc1 is not included in the forcefield you’re using. The forcefields in gromacs have the parameters for the standard nucleic acids and amino acids, but for novel ligands, you often need to retrieve the topology yourself. See Protein-Ligand Complex for a tutorial on how this is usually done

3

Thank you very much

‫‪Karis via GROMACS forums‬‏ <‪notifications@bioexcel1.discoursemail.com‬‏> در تاریخ دوشنبه ۲۴ ژوئن ۲۰۲۴ ساعت ۱۸:۳۱ نوشت:‬

1 Like