Hello, 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.
______________________________ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering "You must be the change you wish to see in the world." --Mohandas Karamchand Gandhi
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