From: Aaron Cann (aaron_at_canncentral.net)
Date: Tue Nov 20 2012 - 13:10:24 CST
Unsubscribe
Sent from my iPhone
On Nov 15, 2012, at 3:56 PM, owner-namd-l-digest_at_ks.uiuc.edu (namd-l digest) wrote:
>
> namd-l digest Thursday, November 15 2012 Volume 01 : Number 918
>
>
>
> In this issue:
>
> namd-l: acylated and amidated parameters.
> Re: namd-l: acylated and amidated parameters.
> Re: namd-l: metadynamics/ABF simulations using collective variables - issues with restarting the calculations
> Re: namd-l: metadynamics/ABF simulations using collective variables - issues with restarting the calculations
> namd-l: How to decide whether an ABF curve has been converged?
> namd-l: Carma v.1.2 released.
> Re: namd-l: How to decide whether an ABF curve has been converged?
> Re: namd-l: How to decide whether an ABF curve has been converged?
>
> ----------------------------------------------------------------------
>
> Date: Wed, 14 Nov 2012 11:45:32 -0600
> From: "Martin, Erik W" <Erik.Martin_at_stjude.org>
> 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
>
> ________________________________
> Email Disclaimer: www.stjude.org/emaildisclaimer
> Consultation Disclaimer: www.stjude.org/consultationdisclaimer
>
> ------------------------------
>
> Date: Wed, 14 Nov 2012 17:20:55 -0600
> From: JC Gumbart <gumbart_at_ks.uiuc.edu>
> Subject: Re: namd-l: acylated and amidated parameters.
>
> 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:
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:46 CST