[gmx-users] Regarding terminal residue parameters (Capping)
sagarbarale at gmail.com
Sat Jul 8 09:43:34 CEST 2017
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
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
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
Mr. Sagar Shivaji Barale
Dept. of Microbiology,
Shivaji University, Kolhapur
416004 MS, India
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