[gmx-users] Ramachandran Plot
spoel at xray.bmc.uu.se
Sun Feb 15 21:35:01 CET 2004
On Sun, 2004-02-15 at 21:24, Mungikar, Amol Arvind (UMR-Student) wrote:
> 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?)
The ramachandran analyses might, due to hardcoded atom names in that
program. ffgmx shoulw work fine though.
> 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.
If you have a stable structure with wrong angles, there maybe something
fishy. If it just happens a short time during your 10 ns, don't worry...
(but do check it!)
> -----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
> 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 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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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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