[gmx-users] About topology for cyclic petide
jalemkul at vt.edu
Wed Dec 26 16:27:54 CET 2012
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 -
> 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
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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