AMBER Archive (2006)

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

Date: Wed Aug 16 2006 - 12:27:23 CDT

('binary' encoding is not supported, stored as-is) 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.


---- 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).

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