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

[David van der Spoel]

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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