There is a very well written tutorial (tutorial B3) on the amber website
based on a 2002 paper by Simmerling et. al.
you can find the section related to what you are interested in doing
(building a peptide from scratch) here:
http://ambermd.org/tutorials/basic/tutorial3/section1.htm
the entire tutorial will likely be helpful:
http://ambermd.org/tutorials/basic/tutorial3/
Jonathan
On Mon, Jun 11, 2012 at 6:09 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
> I would like to model a small peptide with less than 10 amino acids.
> Can I use ptraj or AMBERTools to get the starting geometry for the
> peptide, if yes, what should I do?
> Best regards,
> Catherine
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Received on Mon Jun 11 2012 - 04:00:04 PDT
