[gmx-users] Capping residues

[Justin A. Lemkul]

Sai Pooja wrote:
> Would it be possible to add some capping residues (like --COCH3 and 
> --NHCH3) by writing a separate .itp file and including it in the 
> topology file? Is there a way to make it consistent with charmm forcefield?
> 

No, because you have to specify bonds between these capping residues and your 
protein.  If you're #including them as new [moleculetypes], then you can't add 
these bonds.

> Can this be done alternatively by modifying the .rtp file? If yes, what 
> other operations must one do before using these .rtp files?
> 

Reading in the manual about the file format?  I don't understand your question 
entirely.  All the other force fields use .rtp entries for caps, so I don't see 
why this couldn't be done.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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