[gmx-users] Hen egg white lysozyme.

[Esther]

Viswanadham Sridhara 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?
HETATM's usually aren't found in the database. You have to build a 
topology for the NAG molecule that the Dundee Prodrg server might make 
for you. Check out the protein-ligand tutorial for more info 
http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
> Thanks in advance,
> -Vissu
>
> -- 
> Viswanadham Sridhara,
> Graduate Research Assistant,
> Old Dominion University,
> Norfolk, VA-23529.
> ------------------------------------------------------------------------
>
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-- 
Esther Caballero-Manrique
Graduate Teaching Fellow
Chemistry Department
1253 University of Oregon
Eugene, OR 97403 (USA)
1-541-346-2485