[gmx-users] AFM Pulling index.ndx & pull.ppa

VENKATESH HARIHARAN vuh105 at psu.edu
Sun Jun 29 18:57:50 CEST 2008


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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