AMBER Archive (2006)

Subject: Re: AMBER: DOTA-Lanthanide complexes in Amber

From: Brent Krueger (
Date: Wed Aug 16 2006 - 15:08:57 CDT


What parts of your system's dynamics are you actually concerned
about? If you don't care about the details of the lanthanide or the
protein immediately surrounding it, then you could simply use
targeted MD to restrain that part of your protein, without worrying
about the detailed bonding of your lanthanide. I have done this on a
lanthanide system in the past and was able to use weak restraints
within the TMD, such that there is still reasonable thermal motion
within the restrained region. Dynamics elsewhere in your system
should be fine.

If you do care about accurate dynamics right around the lanthanide,
then I think you need to undertake an extremely difficult
parameterization project. Making the correct number of bonds in Leap
is probably the least of your problems.

Good luck,

On Aug 16, 2006, at 1:27 PM, wrote:

> I would need to form 8 or 9 bonds to one atom, but leap only allows 6
> bonds to originate from a given atom in Amber 7.
> Due to this I made some unusual bonds that give an approximately
> correct
> shape of the molecule, but obviously is not very realistic in terms of
> thermal movement etc.
> Armin
> ---- Original message ----
>>> I have been working on incorporating Gadolinium bound to its DOTA
>>> ligand
>>> into Amber 7. The big problem that needs to be worked out with
>>> this is
>>> the limit on the number of bonds a given atom can form using
>>> Amber 7.
>> Can you be more explicit: what is the problem with a large number
>> of bonds?
>> How many do you need, and where is this imposed? I think this
>> limit is
>> not important (may even be fixed in later versions of Amber).
>> ...thanks....dac
> ----------------------------------------------------------------------
> -
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

Brent P. Krueger phone: 616 395 7629
Assistant Professor fax: 616 395 7118
Hope College SC 2120
Department of Chemistry
Holland, MI 49423

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to