AMBER Archive (2009)

Subject: Re: [AMBER] thymidine monophosphate parametrization

• Previous message: Santosh Mogurampelly: "[AMBER] pulling two atoms in SMD"
• In reply to: case: "Re: [AMBER] thymidine monophosphate parametrization"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

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_at_biomaps.rutgers.edu>:

> On Fri, Jul 24, 2009, Yvonne.Westermaier_at_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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

• Previous message: Santosh Mogurampelly: "[AMBER] pulling two atoms in SMD"
• In reply to: case: "Re: [AMBER] thymidine monophosphate parametrization"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]