[gmx-users] Analysis of mutants

Steffen Wolf swolf at bph.rub.de
Tue Jul 29 17:12:53 CEST 2008

Hi Sundar,
general advice: check the literature on what other people did to get 
insight into similar problems. This should give you a good overview what 
can be done by MD - and what can't. Interaction and fluctuation can be 
assessed via energy analysis (g_energy, one energygroup per amino acid), 
and distance plots (g_dist). Fluctuations are distinguishable via the 
RMSF analysis (g_rmsf). And: check the manual + the GROMACS wiki again.
> hi people,
>          I am new to gromacs. I am running gromacs (version 3.3.1) for a
> protein and its 3 mutants. I am not having any problems in the
> run. I would like to focus my analysis on 3-4 amino acids
> specifically.
> Can anyone please tell me some good commands or a link where I can check
> how these amino acids are interacting, how these amino acids are
> fluctuating etc.
> I searched the manual but I am not sure which commands to use.
> Also, I think it is better to get some help from people who have done this
> type of analysis many times.
> I am waiting for your reply.
> Thank you

Dipl.-Chem. Steffen Wolf
Fellow of the Ruhr-University Research School
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: swolf at bph.rub.de
Web: http://www.bph.rub.de 

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