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

[Justin Lemkul]

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
-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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