[gmx-users] About topology for cyclic petide

Justin Lemkul 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 -
> 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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list