Atomtype modification?

User discussions
1

GROMACS version: 2020
GROMACS modification: Yes/No
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Hi all,
I want to add ions to neutralize my complex and I got this error
ERROR 1 [file topol_DNA_chain_2.itp, line 28]:
Atomtype ON3 not found

I have modified the amber14sb. ff and I think I should add ON3 to the atom type file but I am not exactly sure how to do that

Any suggestion would be appreciated

Thank you

2

Hi,

You can add an atom type also at the begin of the topology file
Have a look at the topology table.

Best regards
Alessandra

3

What species contains ON3? That is not a normal AMBER atom type AFAIK, but it is one in CHARMM. If you’re mixing force fields - don’t.

4

Hi Justin,

ON3 is for the phosphorylated 5’ terminal of DNA . Should I change its name to ON2 which is a normal AMBER atom type ??( I think !!)

I think the best solution is to delete the phosphorylated 5’ terminal of DNA to avoid further problems

5

Nope, ON2 is again a CHARMM type.

I would agree since 5’-phosphate groups are rarely biologically relevant.