[gmx-developers] genvsites

[Erik Marklund]

Hi Erik,

Right. I see your point. I was actually considering making vsite  
construction of hydrogens fully automatic, since there is virtually  
no geometrical data for them in refi_aa.dat, and one will have to  
rely on the force field for their angles etc anyway. Also, as you  
suggest, it would reduce the size of the vsite data file by a fair  
amount. I would however, paranoid as I am, stay away from the input  
structure and rely on the force field for vsite generation.

For the more complicated groups, such as aromatics, It would be nice  
to have one generic data file instead of one for each force field as  
is the case now. It doesn't really comply with the 'mimic the ff'  
idea, but makes it much easier to maintain the vsite data. Then the  
question is whether one really need anything more than what's in the  
current ddb files: angles and bond lengths, that is. All such groups  
are planar anyway, so no VStype has to be provided to the program.  
Masses will always have to be generated, and planarity/symmetry will  
be redundant/irrelevant information.

I will give this some more thought.

Thanks for the input.

/Erik

1 okt 2007 kl. 12.34 skrev Erik Lindahl:

> 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.
>
> Cheers,
>
> Erik
>
> 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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>

_______________________________________________
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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