[gmx-users] Top file modification

[Justin Lemkul]

On 3/21/13 6:30 AM, Shima Arasteh wrote:
> Dears,
>
> As I read in some other messages in mailing list, it is supposed to modify bonds, angles and dihedrals in top file to define a peptide bond for the last and first residues as well as other peptide bonds.
> I am wondering if it is necessary to define pairs too?
>

If pairs are a necessary part of the force field, then yes.  Look at the 
formulation of peptide bonds that you have not messed with to learn what is 
expected.

-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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