[gmx-users] Regarding terminal residue parameters (Capping)

[Sagar Barale]

Dear all,

I am trying to simulate a multichain amino acid structure. PDB ID 2BEG.

I am experiencing problems with the C and N terminal residues i. e. C-ALA
and N-LEU.

An abnormal non-bonded interaction keeps forming between atoms C from ALA42
and N from LEU17.

I tried to cap these residues using acetyl group but i could not assign
proper parameters for the acetylated amino acids.

I tried using -ter flag with all possible protonation states but still the
interactions forms.

I would like to know how can these residues be capped or how can i assign
proper terminal protonation states in order to avoid such long non-bonded
interactions.
-- 
Mr. Sagar Shivaji Barale
Research Scholar
Dept. of Microbiology,
Shivaji University, Kolhapur
416004 MS, India