Re: [AMBER] On the choosing of coordinate for the umbrella sampling

From: Carlos Simmerling <>
Date: Thu, 5 Jun 2014 15:28:32 -0400

a few of our recent articles have done similar things using Amber- they
might give you some ideas.

Li, Huei-Jiun; Lai, Cheng-Tsung; Pan, Pan; Yu, Weixuan; Liu, Nina;
Bommineni, Gopal; Garcia-Diaz, Miguel; Simmerling, Carlos; Tonge, Peter, “A
structural and energetic model for the slow-onset inhibition of the
Mycobacterium tuberculosis enoyl-ACP reductase InhA”, ACS Chemical Biology,
2014, 9 (4), pp 986–993 DOI: 10.1021/cb400896g

Bergonzo, C., Campbell, A., de los Santos, C., Grollman, A and Simmerling,
C. “Energetic Preference of 8-oxoG Eversion Pathways in a DNA Glycosylase”,
J. Am. Chem. Soc., 133, 14504–14506 (2011) DOI: 10.1021/ja205142d

On Thu, Jun 5, 2014 at 7:03 AM, James Starlight <>

> Dear Amber users!
> I'd like to compute of PMF along some coordinate specified transition of my
> protein from the inactive R to the active R* form. I'll be thankful for
> someone who could provide me with some tutorial with the guide for
> calculations of the lowest minimum transition pathway between R and R*
> provided in two pdbs and using it for the further PMF as some collective
> variable (e.g combination of eigenvectors or something like this).
> TFH,
> James
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Received on Thu Jun 05 2014 - 13:00:03 PDT
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