[gmx-users] unknown residue (BGC)

[Justin A. Lemkul]

On 6/13/12 7:48 AM, delara aghaie wrote:
> Dear Justin
> Thanks again for your response.
> About renaming residue would you pls explain more? On which basis I should
> select the new name?
>

The contents of the .pdb file and/or the RCSB website from which you downloaded 
the file will tell you the exact chemical identity of the unknown species.  Once 
you have identified what it is, you can choose a suitable name from the known 
residues in the force field.

> Also about repairing the pdb file, can you pls introduce me a free suitable
> program for this if exists?
>

Spend a few minutes Googling.  You will find numerous potential solutions.

-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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