[gmx-users] Ramachandran Plot
Mungikar, Amol Arvind (UMR-Student)
mungikar at umr.edu
Sun Feb 15 21:25:02 CET 2004
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.
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
> Amol A Mungikar
> Graduate Student
> University of Missouri, Rolla
> MO USA 65401
> Email: Mungikar at umr.edu
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
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
gmx-users mailing list
gmx-users at gromacs.org
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
-------------- next part --------------
A non-text attachment was scrubbed...
Size: 6854 bytes
Desc: not available
More information about the gromacs.org_gmx-users