[gmx-users] Protein Simulations using gromacs

[David Mobley]

Komath,

> 2. What is the common practice to deal with breaks in the protein chains? Is
> it good to terminate each fragment with acetyl groups?

If you are referring to missing residues, these are, of course,
typically present in the protein itself, but just not resolved in some
crystal structures. They are probably in general important for
structure (at least, you can't assume they're not) so you need to
build them in somehow. There are various packages that can do this,
like Modeller.

David

>
>
> Thanks,
>
> Dam
>
> -------------------------------------------
>
> Komath Damodaran
>
> Scientist, Computational Chemistry
>
> Telik, Inc.
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> 3165 Porter Drive
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> Palo Alto, CA 94304
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