<div>Hello,<br><br>I am attempting to use AFM pulling on a 17 amino acid
peptide, but am having trouble with the 'group' concept. I've read the
manual and searched sample XXX.ndx files, but have had no luck. How would
I define the first amino acid as the reference group (i.e. - fixed in space)
and the last amino acid in the peptide as group 1 (i.e. - amino acid at which
the spring acts). The first amino acid is Alanine and the last is
Leucine. Is a sample .ndx file available? The second issue is with
the afm_init value in the pull.ppa file. If I understand correctly
it is the center of mass vector of the peptide, and should go from the
reference group to the pulled group ( from first amino acid A to last amino
acid L). How is this vector calculated and what is the syntax used to
enter this vector in the pull.ppa file. Any help is appreciated.
<br><br>______________________________<br><br>Venkatesh
Hariharan<br>Pennsylvania State University<br>Schreyer Honors
College<br>Undergraduate - Bioengineering<br><br>"You must be the change you
wish to see in the world."<br>--Mohandas Karamchand Gandhi<br><br><br></div>