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
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