GROMACS modification: Yes/No
Here post your question
All of the available ff does not consider the phosphate termini of DNA and RNA
I have tried many amber ff and charm ff but GROMACS keeps giving me fatal error because of no phosphate group at rtp entry. Deleting the phosphate group will solve the problem. Do you have any idea of the consequences of doing so?
adding -ter or nochargegrp might solve the problem . Any suggestions?
I was thinking to parameterize the ff and add a .tdb entry to consider the phosphate group but unfortunately, I don’t know how to do that
if there are any refined ff you recommend or any useful links or tutorials please let me know
Thank you All