[gmx-users] Regarding AIB RESIDUE NOT FOUND IN RESIDUE TOPOLOGY DATABASE

[Mark Abraham]

On 9/01/2012 6:44 PM, ajaniharesh at gmail.com 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