AMBER Archive (2002)

Subject: Re: Questions on crosslinking residues

From: David A. Case (case_at_scripps.edu)
Date: Wed Oct 02 2002 - 18:34:47 CDT

On Tue, Oct 01, 2002, Nicholson, James D Mr ARO wrote:

> I am modelling DNA with a cross-linking agent...
>
> What I did previously was to create a single residue which contained both
> crosslinked residues and the linker. When I imported this into leap, leap
> would correctly (for the most part) assign the atom types, but, I would
> still need to manually repair missed bonds. Apparently, it doesn't much
> like having a main chain that travels through the crosslink and out into the
> other residue.
>

It's a little hard to understand your question without more information.
LEaP does not "assign atom types"; that is done either by hand or through
antechamber. LEaP also doesn't much care what is "backbone" and what is
"sidechain" (although the atoms that link to the previous and subsequent
nucleotides should be the first and last mainchain atoms, as far as I know.)
I also don't know what you did to "manually repair missed bonds": were
these just the cross-linking bonds, or were there others?

Basically, I think more information is needed to be of much help.

> And as a second question; my sequence is palindromic. I would like to
> enforce symmetry during the simulation. Is there an easy way to do this as
> well?

No, Amber does not have this capability.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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