[gmx-users] using gromacs for protein site-mutagenesis study

[Justin A. Lemkul]

Ross KK Leung wrote:
> While replacing large amino acids to small ones may be easy (simply 
> removing redundant atoms=rows in PDB), but how about the reverse 
> direction? Would anybody has any ideas in re-supplementing missing atoms 
> (e.g. glycine to tryptophan)?
> 
>  

You will need an external program, something like Swiss-PDBViewer (DeepView) or 
the "Mutate Residue" extension in VMD.  I am less familiar with the VMD tool, 
but DeepView allows for the selection of a lowest-energy rotamer to optimize 
side chain position.

-Justin

> 
> Thanks a lot
> 
>  
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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