VMD-L Mailing List

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Dec 05 2005 - 10:45:47 CST

What exactly are you doing? If you're trying to analyze the rotational motions of the ring, maybe you can label your atoms so you know if actually the ring is rotating. You can use as template the aromatic amino acids. Phe contains CA, CB, CG and then CD1 and CD2, CE1, CE2 and finally CZ. In this case, you can take either CA-CB-CG-CE1 or CA-CB-CG-CE2 as a reference for the rotational motions of this residue. Thus, you can label every atom of your ring and then, according to your own specifications, track the rotation of your ring.
I hope it helps.
 
Good luck!
Michel

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From: owner-vmd-l_at_ks.uiuc.edu on behalf of andrea spitaleri
Sent: Mon 12/5/2005 9:54 AM
To: vmd mailing list
Subject: vmd-l: discriminate aromatic ring face

Hi all,
how is it possible to discriminate the two sides of an aromatic ring? I need to draw the vector (using orient) normal to the ring plane and see if the vector rotates. Orient package doesn't keep the same orientation of the arrow and so it is difficult to understand if "really" the ring is rotating or not.
Thanks in advance
Regards,

andrea 

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Andrea Spitaleri 
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
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