[gmx-users] unknown residue (BGC)

[Justin A. Lemkul]

On 6/13/12 6:32 AM, delara aghaie wrote:
> Dear Gromacs users
> I want to create from 1AU1.pdb, the  .gro and .top files.
>
> Running this command
>
> pdb2gmx -ignh -f 1AU1.pdb -o 1AU1.gro -p topo.top -water spce
>
> and choose this forcefield:
>
>   GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>
> I get this error:
> Fatal error:
> Residue 'BGC' not found in residue topology database
> How can i fix it?
>

http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

In this case, simply renaming the residue is probably all that is necessary. 
53A6 has parameters for sugars.

> Also what this message by pdb2gmx means?
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
> 8 out of 8 lines of specbond.dat converted successfully
>

There are missing residues in the PDB structure.  The header of the file tells 
you which ones are missing.  You will need to reconstruct their positions with 
some external modeling software before proceeding.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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