From: Molybdos Kirkimpolakis (supercomputer.simulation_at_gmail.com)
Date: Tue Aug 02 2011 - 14:11:49 CDT

Dear VMD Masters,

I want to select the sugars in my protein using VMD but it seems that VMD
does not recognize them. I am using Amber force field because my protein has
important sugars that I cannot delete. Can you help me to select the sugars?

Let's say I want to set zero the beta factor of the sugars I do the
following

set allatoms [atomselect top all]
$allatoms set beta 0
set atomsugar [atomselect top sugar]
$atomsugar set beta 1
$allatoms writepdb new.pdb

However when I see in the pdb the beta factor of the sugars; they are still
zero.

can anyone help me out.

Thanks so much

-- 
cheers
Πανεπιστήμιο Πατρών <http://www.biology.upatras.gr>
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Molybdos Kirkimpolakis