Re: peptide structure

From: ipsita basu (
Date: Thu Jan 27 2011 - 02:29:21 CST

Thank you for your reply. I found that the structure of the peptide
may change depending upon the environment. So the system is ok.

But we have another problem. We have a machine configured as:
Linux compute-00-02.pcm 2.6.18-194.el5 #1 SMP Tue Mar 16 21:52:39 EDT
2010 x86_64 x86_64 x86_64 GNU/Linux
which has 8 nodes,they can be connected from the master node by
ssh,but the problem is that we can't submit any job from master
node,we have to login to individual node and then have to submit it by
using the command:
./charmmrun ++local +p4 ./namd2 input > output&
Can you please help me to find out how to submit job from master node properly?
Thank you again.

On 1/23/11, Chris Harrison <> wrote:
> 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.
> Best,
> Chris
> --
> 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

Ipsita Basu
Research Fellow
c/o : Dr. Chaitali Mukhopadhyay
Rajabazar Science College
92 APC Road
Kolkata - 700009

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