[gmx-users] kindly guide me!

[Anton Feenstra]

Dallas B. Warren wrote:
>  > Is it possible to   visualize the same in the INSIGHT II before
> entering into simulation or solvation step? 
>  
> ? Not sure what you are asking there.  Depends on what file formats you
> can load into Insight, if it can handle the *.gro file, then you can
> load and view it.

Pretty sure insight doesn't read .gro.
Use 'editconf -f this.gro -o that.pdb' to convert.


>>Is there any other molecular visualisation tool for viewing   the
> molecule? 
>  
> There are plenty, few have been mentioned on this emailing list, so try
> a search.

Gromacs comes with the simple trajectory viewer 'ngmx', which has the 
advantage of showing bonds as they are defined in the topology.

For quick and simple work, I use rasmol.


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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