VMD-L Mailing List
From: Molybdos Kirkimpolakis (supercomputer.simulation_at_gmail.com)
Date: Tue Aug 02 2011 - 14:11:49 CDT
- Next message: AB: "vmd 1.9 sur doesn't work"
- Previous message: John Stone: "VMD User Survey coming to your email inbox soon...."
- Next in thread: John Stone: "Re: selection of sugars with VMD"
- Reply: John Stone: "Re: selection of sugars with VMD"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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> ΤΜΗΜΑ ΒΙΟΛΟΓΙΑΣ Molybdos Kirkimpolakis
- Next message: AB: "vmd 1.9 sur doesn't work"
- Previous message: John Stone: "VMD User Survey coming to your email inbox soon...."
- Next in thread: John Stone: "Re: selection of sugars with VMD"
- Reply: John Stone: "Re: selection of sugars with VMD"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]