AMBER Archive (2009)

Subject: Re: [AMBER] thymidine monophosphate parametrization

From: case (
Date: Mon Jul 27 2009 - 09:47:38 CDT

On Fri, Jul 24, 2009, 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

And, are you sure you should have two OH groups? I'd think(?) this would only
occur under very acidic conditions.


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