[gmx-users] Ramachandran Plot

[Mungikar, Amol Arvind (UMR-Student)]

Thank you Dr.David van der Spoel  for your reply. Here are few more details:
I am using GROMACS force field. (I was thinking why you asked this question, is the force field change going to give me different results?)
One thing I forgot to mention in my previous message was that the peptide is charged with a charge of -4e. Can this be the reason (or artifact) for the results in this MDRUN i made? Infact I am running the same peptide with four Sodium ions to see if I can find out any major difference. 
I checked the structure again, and nothing seems to be wrong with the positioning of atoms of the peptide - in terms of overlapping with water molecules or peptid atoms itself. N-terminal of the peptide is elongated. Infact all the dihedral angles are in accordance with the structure. As you said maybe the structure is correct, I need to analyze all other results such as RDF,Energies etc before coming to any conclusion though. Meanwhile thank for your help. 
Sincerely,
Amol

	-----Original Message----- 
	From: gmx-users-admin at gromacs.org on behalf of David 
	Sent: Sun 2/15/2004 12:07 PM 
	To: gmx-users at gromacs.org 
	Cc: 
	Subject: Re: [gmx-users] Ramachandran Plot
	
	

	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.
	________________________________________________________________________
	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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