From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Wed Nov 14 2012 - 11:52:05 CST

These parameters exist in the charm forcefield. they are found as residue patches, ACE, ACP, CT1,CT2,CT3

Brian

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From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Martin, Erik W [Erik.Martin_at_stjude.org]
Sent: Wednesday, November 14, 2012 9:45 AM
To: Namd Mailing List
Subject: namd-l: acylated and amidated parameters.

Hi, I was wondering if anyone knew of any generic parameters for acylated and amidated amino acids. I'm thinking of simulating binding of some small peptides a colleague of mine measured experimentally – when he had the peptides synthesized he had them N-terminal acylated and C – terminal amidated. If anyone knows of some parameter sets, it would make my life easier. I'd use either charmm or amber.

Thanks,
Erik

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