VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Feb 12 2009 - 06:21:11 CST

Hi Bo,

You need an atom selection for the atoms that should be mobile. The
keywords are in the manual (
http://www.ks.uiuc.edu/Research/vmd/current/ug/node79.html); you
probably want to use sidechain.
Best,
Peter

bo baker wrote:
> Hi, John:
>
> I would like the backbone to be fixed, only side chains to be minimized.
>
> I can set up the pdb with CA "fixed" by Tcl, but I don't know what to
> type with NAMD GUI interface?
>
> Thanks
>
> Bo
>
> On 2/9/09, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>> Bo,
>> I believe you're supposed to select that atoms that
>> are mobile (i.e. not fixed). Thus the default value of "all".
>>
>> Cheers,
>> John
>>
>>
>> On Mon, Feb 09, 2009 at 09:17:15AM +1100, bo baker wrote:
>> > Hi, VMD:
>> >
>> > I would lile to use NAMD GUI interface to set up energy minimization
>> > on side chains with CA fixed. Which words should be typed in the
>> > "select fix and mobile atom"?
>> >
>> > Thank you for your advice
>> >
>> > Bo
>>
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>>
>>