[gmx-developers] genvsites

Erik Lindahl lindahl at cbr.su.se
Mon Oct 1 12:34:18 CEST 2007

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.

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.



On Oct 1, 2007, at 11:03 AM, Erik Marklund wrote:

> Hi,
> I've put some text on the wiki for genvsites (http:// 
> wiki.gromacs.org/index.php/Genvsites) describing the current state  
> of things. We've decided to make a force field independent  
> description of the virtual site constructions, which does not  
> contain much geometrical nor topological information. Ideal  
> geometries will be constructed from refi_aa.dat, containing  
> crystallographic bond/angle/tortional data, from which in turn  
> center of mass and moment of inertia will be calculated when  
> needed. We're aiming to make the program 'stupid', i.e. not make  
> too many assumptions or smart decisions, and just read and  
> interpret the vsite data file. Some information will be taken from  
> the topology, and perhaps also from the force field in special  
> cases. Any comments on the proposed file format or the overall  
> strategy is greatly appreciated.
> Over and out.
> _______________________________________________
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,	75124 Uppsala, Sweden
> phone:	+46 18 471 4537		fax: +46 18 511 755
> erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys
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