Still can't build NMA in GROMOS - help please!

User discussions
1

GROMACS version: 2016
GROMACS modification: No

Hello!

I am trying to build a topology with GROMOS54a7 for N-methyl acetamide (ACE and NME residues). GROMOS doesn’t seem to recognize NME. Does it have a different name in GROMOS? A while ago someone from the GROMACS help forum gave me an rtp file for NMA (below), but when I include it in my current directory pdb2gmx doesn’t seem to see it. What (else) do I need to do to have GROMOS recognize my NMA molecule? I know that people have done simulations of NMA in GROMOS force fields before, and they didn’t report needing to do anything special to make it work. What am I missing here?

Thank you!
Dan

[ 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

2

Add the .rtp entry to aminoacids.rtp, add NME as a Protein entry in residuetypes.dat, and choose ‘None’ for the C-terminal type when prompted by pdb2gmx. Your input coordinate file needs to have a separate NME residue at the C-terminus, since pdb2gmx has no ability to build it.