[gmx-users] Top file modification

[Justin Lemkul]

On Tue, Mar 19, 2013 at 1:36 PM, Shima Arasteh
<shima_arasteh2001 at yahoo.com>wrote:

> Would you please let me know if it is acceptable to add dihedrals and
> angles and bonds? and not to add any pairs to the top? just deleting the
> pairs which are added by pdb2gmx incorrectly to the terminus?
>
>
> And I don't know that if I don't add all bonds or dihedrals what would
> happen? How would I be sure that I have added all modifications completely?
>
>
All you're doing is creating a peptide bond like any other. Its description
should be identical to any other peptide bond in the protein. An incorrect
or incomplete description of the newly created peptide bond would mean an
unreliable physical model that would either crash or produce spurious
results.

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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