[gmx-users] Hen egg white lysozyme.

[Viswanadham Sridhara]

Hi David,
I could figure out that parameters for NAG are not that important. So, I
deleted them and used pdb2gmx to get the topology.
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?
Thanks in advance.
-Vissu.

On 8/8/06, David Mobley <dmobley at gmail.com> wrote:
>
> 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> 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.
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read
> > http://www.gromacs.org/mailing_lists/users.php
> >
> >
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Viswanadham Sridhara,
Research Assistant,
Old Dominion University,
Norfolk, Va-23529.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060810/fcf2bf47/attachment.html>