[gmx-users] About topology for cyclic petide

[Justin Lemkul]

On 12/26/12 9:50 AM, vidhya sankar wrote:
> Dear justin
>
>                  Thank you for your Previous reply
> I Have Successfully constructed topology for cyclic peptide  using spce bond and Other Appropriate Changes in the . top files
>
> Yet I Want to make CO Terminal  But When I interactively Choose the Terminal  By pdb2gmx  It Shows Only
>
> 1)COO -
> 2)COOH
> 3)None
>
> I want to Make One more Choice Namely CO For C-Terminal Residue of (LAst Residue ) My Cyclic Peptide
>
> It Adds One Two oxygen atom on the Carbon Atom (O1 & O2) . But I Need the Addition Of One Oxygen Atom
> How to Do It ?

It sounds like you made the wrong choice.  The proper selection is "None" such 
that your C-terminus is treated like any internal residue and is engaged in a 
peptide bond with the N-terminus.  The actual bond in this case is defined in 
specbond.dat since pdb2gmx can only otherwise handle linear sequences of residues.

>   Which Database file  Should I EDIT ? .C Terminal Data Base
>

You don't need to edit anything, you only need to use the terminus selection 
mechanism correctly.

-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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