Re: [AMBER] Lipid linked to a peptide

From: David A Case <>
Date: Tue, 7 Jul 2015 11:23:46 -0600

On Tue, Jul 07, 2015, Arnoult, Eric [JRDUS] wrote:
> I'm interested to run an MD simulation for a non-native peptide. One of
> the residue is covalently linked to a lipid.
> What should be the best approach to define the new non-natural residue?
> Do I need to create two new residues (one for the amino acid linked to
> the lipid, one for the lipid) or just one for the amino acid bonded to
> the lipid?

You can go either way, but I would tend to favor the second choice (just
because it is simpler, but that is a subjective opinion). See
Tutorial B5 for an example of creating a modified residue.

...hope this helps....dac

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Received on Tue Jul 07 2015 - 10:30:02 PDT
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