Thank you for your helpful comments. Under physiological conditions,
having 2 OH in a phosphate group does not make sense. Parametrization
with just 1 OH works fine.
Quoting case <case.biomaps.rutgers.edu>:
> On Fri, Jul 24, 2009, Yvonne.Westermaier.unige.ch wrote:
>>
>> Using Amber9, I am currently trying to parametrize thymidine
>> monophosphate correctly. During a minimization-equilibration in NAMD,
>> the 2 OH groups of the phosphate group get too close to each other.
>
> First, you probably will need to put vdW radii on the hydrogens, or otherwise
> keep them from getting too close to another oxygen atom on the same
> phosphate.
> It's probably a good idea to see what people have done with AMP or GMP as a
> start.
>
> And, are you sure you should have two OH groups? I'd think(?) this
> would only
> occur under very acidic conditions.
>
> ...dac
>
>
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Received on Tue Jul 28 2009 - 10:08:50 PDT
