[gmx-users] end capping
x.periole at rug.nl
Sat Dec 7 17:27:06 CET 2013
You can choose different termini by setting the option term (-term) to pdb2gmx.
The ff gromos 53a6 has a strong tendency to destabilize alpha helices and favors sheets. If you like to stick to gromos ff you need to switch to the 54a7 more recent version to which a rectification of this bias has been attempt.
> On Dec 7, 2013, at 14:11, Shine A <shine.a at iisertvm.ac.in> wrote:
> I am using MD to study the folding of peptides. Now I want to
> modify N terminal of the peptide with acetyl group and C terminus with
> amide group.How Can I do this? What are the changes I should made in
> various files? Gromos96 53a6 is using for simulation.
> Thank in advance
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