[gmx-users] Ramachandran Plot

David spoel at xray.bmc.uu.se
Sun Feb 15 20:05:01 CET 2004

On Sun, 2004-02-15 at 19:09, Mungikar, Amol Arvind (UMR-Student) wrote:
> dear gmx-users,
> This may sound very trivial! But, here it goes ...After solvating a
> small 8-residue peptide (there is no glycine in my peptide) in water for
> 10 ns, the peptide structure I am getting at the end of 10ns shows
> torsion angles phi and psi angles going in the disallowed regions of
> Ramachandran Plot. Well, I know that this is not the 'representative'
> structure of the peptide! But, is there any way to avoid going in the
> disallowed regions of the Ramachandran Plot, or maybe I am doing
> something wrong!! 
> Is there any way I can constraint only the omega (C-N) angle while
> keeping phi and psi free?
Usually omega is fine, but you can check that too using g_chi -omega.
Which force field do you use?

> I request all of you to kindly help me understand the concept. Thank you
> very much in advance.

Either there is an error in your topology or these structures are
correct... Have you checked the structure corresponding to the violated
ramachandran angles?

> Amol A Mungikar
> Graduate Student
> University of Missouri, Rolla
> MO USA 65401
> Email: Mungikar at umr.edu
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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