Re: acylated and amidated parameters.

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Nov 14 2012 - 17:20:55 CST

In the charmm forcefield, you can use the patches ACE and CT2 for first and last, respectively, instead of the default NTER and CTER, when building your segments in psfgen. I tend to do this for all proteins to avoid introducing additional charges at the termini.

On Nov 14, 2012, at 11:45 AM, Martin, Erik W wrote:

>
> 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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