[gmx-developers] genvsites

Berk Hess hessb at mpip-mainz.mpg.de
Mon Oct 1 13:30:07 CEST 2007

Erik Lindahl wrote:

> Hi Erik,
> David and I spoke about this last friday, and I'm not sure I agree 
> completely :-)
> First, this approach is just moving the problem. Instead of having to 
> create dummy settings for each force field you end up having to 
> specify dummy parameters for each new molecule/residue. This will 
> really be a pain for people working with small organic compounds, etc.
> The current aromatic vsites are horrible (construction-wise, I'm not 
> even thinking about their usefullness...) and should be replaced, but 
> the "standard" hydrogen vsites can actually be constructed completely 
> automatic for new molecules.
> I've looked at quite a few vsites manually the last couple of days, 
> and the largest deviations by far occur in peptide groups and similar 
> constructs that aren't exactly planar in reality, but the vsite 
> construction forces them to be. There's nothing we can do about that, 
> and in comparison the deviations between ideal and force-field values 
> e.g. for CH2 angles are very small.
> The other problem concerns e.g. NH2 groups. If I recall correctly 
> these are sometimes planar in Gromos96, while OPLS/Amber model them as 
> non-planar. In my opinion the right thing to do in that case is to 
> model the force field as good as possible, since the point is to 
> remove degrees of freedom while altering as little as possible. 
> Otherwise we should for consistency also alter the constraint lengths 
> of all bonds to agree with experimental structures rather than the 
> equilibrium values in the force field.
I can remember a discussion on this, but I think NH2 are should be and 
are always planar.

> So, it's definitely worth cleaning up, it would be nice to generate 
> the MC/MN dummy mass parameters automatically from the force field 
> (easy), and then create a residue-specific database for "advanced" 
> constructs such as virtual aromatic sidechains. I still think it's 
> more correct to set the simple vsites from the force field, though, or 
> possibly the input structure.
I agree.

I don't know about the usefulness of vsite aromatics.
I have never used them and will probably never use them.
So as far as I am concerned they could be removed,
but maybe some people do use them.


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