AMBER Archive (2007)

Subject: AMBER: Atoms closer to 2 angstroms to each other

From: Christopher Gaughan (clgaughan68_at_gmail.com)
Date: Mon May 07 2007 - 09:38:06 CDT

Dear all,

I am modeling two 28aa artificial peptides that aggregate into a
coiled-coil. To do this I have taken the side chains off tropomyosin and
replaced them with the side chains of interest. In one model I have the two
strands of tropomyosin composed of 8mers- specifically- strand one is
composed of an 8mer of the type 1 peptide and strand 2 is composed of an
8mer of the type 2 peptide. I would like to put a TER card after each 28aa
mer in each strand to simulate the strand being composed of 8 distinct
units. When I do so, Amber just reconnects them. I assume this is because
the consecutive C and N termini I wish to simulate are too close together.
Is there any way I can get around this automatic feature (connecting atoms
that are very close) in AMBER 8?

Thanks for any advice,
Chris

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