GROMACS version: 2016.5-foss-2018b
GROMACS modification: No
A while ago I posted a question about whether it is possible to use N-methyl acetamide with the GROMOS96 53a6 force field and no one answered and my question was greyed out for some reason. I just want to know if there is any way GROMOS96 can support a NME (N-methyl cap) residue for N-methyl acetamide, considering it is not in the force field specification (unlike ACE) but people in the literature have used GROMOS96 53a6 for NMA successfully so I don’t know…
Thank you!
Dan
This is an rtp entry for NME with GROMOS 54A7 I made ages ago (so worth checking it is correct yourself):
[ NME ]
[ atoms ]
N N -0.31000 0
H H 0.31000 0
CA CH3 0.00000 1
[ bonds ]
N H gb_2
N CA gb_21
[ angles ]
; ai aj ak gromos type
-C N H ga_32
-C N CA ga_31
H N CA ga_18
[ impropers ]
; ai aj ak al gromos type
N -C CA H gi_1
[ dihedrals ]
; ai aj ak al gromos type
-CA -C N CA gd_14
Unless there is a good reason, I would not recommend using GROMOS 53A6 for protein/peptide simulations but a more recent GROMOS force field version.
Cheers
Tom