Fwd: [gmx-users] Hen egg white lysozyme.

[Viswanadham Sridhara]

Hi David.
I thought of the same and I started running it using angular mode yesterday.
Thanks though for a quick feedback.
-Vissu

On 8/11/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Viswanadham Sridhara wrote:
> > Hello everyone,
> > I could figure out that parameters for NAG are not that important. So, I
> > used free HEWL.
> > I started running it, but I realize that the protein started to rotate
> > around the center of mass with a frequency of around 200ps.
> > I used "Linear" as an option for comm_mode and I used "Protein" in
> > comm_grps.
> > Any reason Why the protein is rotating around its center of mass, is it
> > normal?
>
> yes.
>
> comm_mode = angular
>
> > Thanks in advance.
> > -Vissu.
> >
> > ---------- Forwarded message ----------
> > From: *David Mobley* <dmobley at gmail.com <mailto:dmobley at gmail.com>>
> > Date: Aug 8, 2006 12:32 AM
> > Subject: Re: [gmx-users] Hen egg white lysozyme.
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org
> > <mailto:gmx-users at gromacs.org>>
> >
> > Vissu,
> >
> > Depends on what you are trying to do. Many proteins deposited in the
> > pdb contain "uninteresting" ligands bound to them (i.e. cosolvent
> > molecules, etc.) On the other hand, sometimes ligands are functionally
> > important or significantly affect the structure. You have to decide
> > whether you want to include NAG or not; it might help to first figure
> > out what it is and what it's used for (perhaps look up its name, and
> > look at the paper and PDB headers...).
> >
> > It is obviously harder to come up with parameters for NAG than not. If
> > you end up deciding it's not important, you can, for example, just
> > remove the HETATM entries dealing with it before running pdb2gmx.
> >
> > David
> >
> >
> > On 8/7/06, Viswanadham Sridhara < muta.mestri at gmail.com
> > <mailto:muta.mestri at gmail.com>> wrote:
> >  > Hi Everyone,
> >  > I am trying to simulate a protein and I am getting the following
> error
> >  > message.
> >  > "NAG" not found in residue topology database. I checked gmx-users
> > discussion
> >  > list to find out if someone ever used 1HEW.pdb . Its a hen egg-white
> >  > lysozyme. I did not get even a single archive about this.
> >  > It is under HETATM section of .pdb file. Any help is appreciated.
> >  > I know that I have to add this residue in aminoacids.dat file and
> create
> >  > atoms and bonds in .rtp section. Is there any other way around?
> >  > Thanks in advance,
> >  > -Vissu
> >  >
> >  > --
> >  > Viswanadham Sridhara,
> >  > Graduate Research Assistant,
> >  > Old Dominion University,
> >  > Norfolk, VA-23529.
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> > --
> > Viswanadham Sridhara,
> > Research Assistant,
> > Old Dominion University,
> > Norfolk, Va-23529.
> >
> >
> > ------------------------------------------------------------------------
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>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
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-- 
Viswanadham Sridhara,
Research Assistant,
Old Dominion University,
Norfolk, Va-23529.
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