[gmx-users] more than one protonation per residue with pdb2gmx

[Justin A. Lemkul]

On 7/12/12 6:12 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi Justin,
> so you mean that I first have to add the capping groups to my structure
> and then run pdb2gmx with the -ter function?
>

Yes.  The capping groups (see your force field's .rtp file for available 
entries) are treated as any other residue.  Gromacs will not magically build 
them; they need to be present.

> But how can I add the capping groups to the structure?
>>

You'll have to use some external modeling software for that.

-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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