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

[VENKATESH HARIHARAN]

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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