AMBER Archive (2002)

Subject: Questions on crosslinking residues

From: Nicholson, James D Mr ARO (James.Nicholson_at_apg.amedd.army.mil)
Date: Tue Oct 01 2002 - 16:59:19 CDT

I am modelling DNA with a cross-linking agent. I need to generate a residue
template which will be recognized by leap. However, the whole
mainchain/sidechain paradigm that Amber uses doesn't look like it can handle
this type of crosslink.

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.

My question: is there a better way to do this?

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?

-Jim Nicholson
USAMRICD