From: Aditya Padhi (
Date: Tue Jun 16 2015 - 14:03:15 CDT

Dear VMD Users,

I am working on a protein, which is known to cleave few GPI-anchor proteins
(Glycosylphosphatidylinisotol). Also, I know that there are several other
candidate GPI-anchor proteins which may or may not be cleaved by my protein
of interest. I was wondering, if there is any tool/method in Amber using
which I can atleast get some preliminary information on which of the
proteins that could be probably cleaved by my protein of interest.

The 3D structure of my protein of interest and most of the GPI-anchor
proteins is not available. I was therefore wondering if there is any such
tools/methods available that I am missing using which I can find out which
of the GPI-anchor proteins are being cleaved.

Any suggestion/guidance would be highly appreciated.

Thank you so much,