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 ha
On 12/7/13 8:11 AM, Shine A wrote:
Sir,
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 s
Sir,
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
