[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Justin Lemkul jalemkul at vt.edu
Wed Dec 5 19:50:16 CET 2012

On 12/5/12 1:39 PM, James Starlight wrote:
> Justin,
> Indeed the force field is the 54a7 ( modiffied version of the 54a6).
> The main reason of using GROMOS ff in that case was the topology of
> ligands which could be easily created by means of prodrg or ATB. On
> other hand I've never worked with the protein-ligand complexes in
> charmm ff for instance.

Well, you get out what you put in.  A recent paper 
(dx.doi.org/10.1002/jcc.23055) showed that Gromos force fields performed very 
poorly for simulating nucleic acids.  There are others, but that's just a recent 
one.  If you're choosing a force field because it makes life easy, be prepared 
to defend your results if they are of poor quality or defend a lot of wasted 
time while you re-do the simulations :)

There are servers that produce CHARMM topologies and other programs that will 
convert AMBER topologies into Gromacs format as well.  I would suggest you 
evaluate all the options available.

> By the way is there any suitable builing blocks (implemented in the
> rtp enties of the gromos ff) which could be used for charge
> assignment?

That depends on the functional group.  If it's also found in proteins, yes.  If 
not, then maybe but probably not.


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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