[gmx-users] Protein-Ligand Interactions

[Tsjerk Wassenaar]

Hi Mitch,

Not sure whether anybody has the topologies lying around, but in order
to get the behaviour of the carbohydrate rings right, you need to have
the sugar parameters from the GROMOS 45a3 (or later) force field from
Roberto Lins and Wilfred van Gunsteren. Depending on the length of the
NAG chain, maybe it's best to define the building blocks in the
ffG*.rtp file. Alternatively, you can generate a topology for NAG by
hand, using the sugar building blocks present in ffG43a5.rtp,
ffG53a5.rtp or ffG53a6.rtp as a template. Do make sure to use the
correct bond/angle/dihedral definitions, since things have changed
between these force fields and 43a2. Also, if you manage, please share
your building blocks/NAG topology through the users contribution
section of the gromacs site.

I'm not even sure if this helps you a lot. As you see, it can take
quite a bit of effort to get a topology for a non-standard molecule,
especially if you want to get it "right".

Best,

Tsjerk


On 10/20/06, Mitchell J Stanton-Cook <s4026869 at student.uq.edu.au> wrote:
> 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
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336