[gmx-users] g_mindist

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Mar 16 13:40:43 CET 2007

Hi Ozge,

'sidechain' indicates all side chains present in your system, i.e.
everything designated 'protein' based on residue names, excluding
everything taken to be 'backbone' based on atom names.

You'll probably have to run the program three times to get the
combinations of minimal distances between your side chains, using
appropriate index groups.



On 3/16/07, OZGE ENGIN <OZENGIN at ku.edu.tr> wrote:
> Hi,
> I forgot to ask  my other question :) When I use the g_mindist command, it asks me to select two groups for which the distance will be calculated. I am confused for the following: I want to calculate the minimum distance among three side chains of my molecule in all combinations. So, if I choose the side chain (system 8) option for this command twice, which side chains will be taken into consideration?
> Thanks in advance
> Ozge Engin
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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