Re: peptide structure

From: Chris Harrison (
Date: Sun Jan 23 2011 - 10:10:08 CST

Dear Ipsita,

The most likely explanation is that the backbone contains stress in its
fixed state, and that upon releasing it the resulting forces are simply
stronger than those of the surrounding system (which at 25ns, I am
presuming is equilibrated). You should ensure that the surface
tension / area-per-lipid of your lipid membrane is appropriate for the
given lipid type, attempting to match known values. If you then release
the restraints more slowly, you may find the 2nd-ary structure is retained.
If not, and you have solid evidence that the 2nd-ary structure _should_
be retained in the environment of your simulation, then there is likely
something pathological in your protein's structure -- check your phi/psi
values, backbone h-bonding patterns in helices and sheets, missing
disulfide bonds or key salt-bridges, etc.


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                          Voice: 217-244-1733              Fax:   217-244-6078
ipsita basu <> writes:
> Date: Wed, 19 Jan 2011 10:35:34 +0530
> From: ipsita basu <>
> To: namd-l <>
> Subject: namd-l: peptide structure
> Sir,
>     I have a lipid membrane -peptide system which I equilibrated for
> 25 ns keeping the backbone of the peptide fixed. When I reduce the
> force value slowly in the fix atom file, the structure of the peptide
> is ok but when I set the fix atoms option off, the secondary structure
> of the peptide breaks.
> Can you please tell me what is the proper reason behind it? Is there
> any option to change in the input script ? Thank you. Waiting for your
> reply.
> -- 
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009

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