[gmx-users] Analysis of mutants

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Tue Jul 29 17:13:10 CEST 2008


On Tuesday, 29. July 2008, N. Sundar Ram wrote:
> 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

a good starting point is the manual and the wiki of gromacs 

Analysis tools you can use are something like

g_rms g_dist ...


 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
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 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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