On 9/01/2012 6:44 PM, [email protected] wrote:
Hello sir,
I am using gromacs 4.5.3 version.
I am doing 12 amino acid peptide simulation. But my peptide have some non
standard amino acid like AIB,NLE
After fire pdb2gmx comand i am getting follwing error in simulation.
''Residue NLE not found in residue topology database.''
What to do next for this error ?
See
http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
<http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database>
Can I have to use prodrg for non standar amino acid ?
Possibly, but you will have to convert some file formats to use it with
pdb2gmx, and it is unwise to rely on the results of PRODRG without
further testing.
Mark
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