-NH2 and -COOH termini in AMBER force field

User discussions
1

Dear Gmx users,
I would like to use -NH2 and -COOH termini for a peptide in my simulations. How can I use these termini with Amber force field?
I found residues named NHE and NH2 both similar in aminoacids.rtp file in an Amber force field.
Is there any possibility to use COOH terminal?

Best regards,

Mijiddorj

2

Appreciate any advice.

Best regards,
Mijiddorj

3

AMBER force fields are special in that they do not make use of normal terminal patching; individual N- and C-terminal residues have to be defined. If they’re not in the .rtp file, they’re not supported by GROMACS natively. If topologies exist (e.g. in the original AMBER files or published elsewhere), you will have to write new residue entries yourself.

4

Dear Justin,

Thank you very much for your reply.

Best regards,

Mijiddorj