[gmx-users] How to handle incomplete PDB file?

[Justin A. Lemkul]

Lee Soin wrote:
> Hello!
> While processing a PDB file, pdb2gmx ended up with the warning
> 
> WARNING: atom CG not found in residue 14 while adding atom
>  
> and the error
>  
> Fatal error:
> Atom CG not found in residue ASP14 while adding hydrogens
>  
> Specifying -missing in pdb2gmx doesn't work.
>  
> In the original PDB file, a few missing atoms are listed.
>  
> What to do in this situation?
> 

Rebuild them with modeling software.

-Justin

> -- 
> Sun Li
> Department of Physics
> Nanjing University, China
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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