VMD-L Mailing List

From: Alexandre Barrozo (barrozo.ah_at_gmail.com)
Date: Mon Dec 05 2016 - 18:39:01 CST

Dear all,

I have this xyz file that has two large molecules, and the ordering of the
atoms is completely mixed, so that, for instance atom 1, 2 and 5 are from
molecule A, and atoms 3, 4 and 6 are from molecule B. When I run the GUI of
VMD, I can move the structures separately by pressing 7 and clicking on one
of the molecules. Is there a smart way for VMD to recognize these two
molecules and renumber in a way that I have all the atoms belonging to a
single molecule being all together, and then the atoms of the second
molecule follow afterwards, like atoms 1, 2 and 3 belonging to molecule A,
and 4, 5 and 6 to B?

Thanks in advance,

Alexandre