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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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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