AMBER Archive (2005)

Subject: Re: AMBER: How to insert a protein in lipid bilayer

From: Yong Xu (yxu_at_mail.sioc.ac.cn)
Date: Wed Jul 27 2005 - 20:47:22 CDT

Dear nag raj

please find this link of Sansom group:http://sansom.biop.ox.ac.uk/
there are many papers on transmembrane protein in lipid, expecially K+ channel.

you may read those paper and found something interesting.

if I remember correct, resdiues Tyr and Trp should be position near the membrane-water interfaces.
you should firstly put the lipid block into correct position, align the symmetrical axis of lipid to the x,y,z aixs. you need also to align the main axis of protein (if have) to the z (or x, y). then tranform align x and y to put protein into suitable position in lipid. those lipid molecules with close contact with protein should be deleted.

you may also search the Gromacs mailling list to find something about this issue.

======= 2005-07-27 09:56:00 nag raj wrote£º=======

>Dear amber users,
> How to insert protein in lipid bilayer?
> Thank you
> nagaraju

regards!

Yong Xu
¡¡¡¡¡¡yxu_at_mail.sioc.ac.cn
¡¡¡¡¡¡¡¡2005-07-28
===========================================================
* Yong Xu
* State Key Lab of Bioorganic & Natural Product Chemistry
* Shanghai Institute of Organic Chemistry
* Chinese Academy of Science
           
* 354 Feng Lin Road, Xu Hui District
* Shanghai, 200032, China
        
* Email: yxu_at_mail.sioc.ac.cn
* yxuemail_at_sina.com
===========================================================
¡¡¡¡¡¡¡¡¡¡¡¡

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu