[gmx-users] Protein-Ligand Interactions

[Mitchell J Stanton-Cook]

Hi All.

I wish to analyse the dynamics of t4 Lysozyme with a small peptide
attached via a disulphide bond.

My MD runs are fine, however I wish to add the ligand N-acetyl
glucosamine (NAG) in the active site to measure some distances from the
attached peptide to the NAG molecule.


I have initially followed John Kerrigan's Drug-Enzyme complex tutorial.


ie. Use ProdRG3 sever to generate a gromos87 .itp for NAG, edit the
target.gro, to append the NAG atoms, edit target.top and add:
#include "nag.itp" and
[ molecules ]
NAG       1



My problem comes about, I wish to use the GROMOS96 forcefield (from what
I have read only the GMX force field works) and when I run grompp I get
complaints about a missing atom "CS2".

>From searching this archive I see:
* I need to modify nag.itp to be GROMOS96 compatible. (NOTE: when
comparing an example GROMOS96 .itp to the GROMOS87 .itp there does not
seem to be any significant differences besides formatting).

Can someone point me in a direction of how to go about this?

Can I edit ffG43a1.atp and add these missing atoms?

Furthermore, has anybody successfully done something similar to this -
performing a simulation with t4Lys:NAG?


Any help would be appreciated

Cheers Mitch