[gmx-users] question about DNA simulation 5'&3' ends

[K.A. Feenstra]

Luke Czapla wrote:
> Hi David,
> 
>   Aren't the tdb files specific to proteins?  I can't use them because of
> the point that they are -c and -n for C and N terminii.  I'm talking about
> the 5' phosphate group and the 3' hydroxyl group.  I don't see any kind of
> syntax you could use in a tdb file, but if you have any idea, let me know,
> because I know which atoms to remove/add, but not the basic concept of
> using a tdb file for DNA or RNA.

The '-n' and '-c' obviously makes no sense for DNA, but the principles
should be generally appliccable, if you know that the 'N' is the starting
and the 'C' the finishing terminus. Furthermore, there are sections for
atoms to be removed, added and replaced, and for bonded parameters (bonds,
angles etc.) to be specified. IIRC, this all is explained in the paper
manual.


-- 
Groetjes,

Anton
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|        | Anton Feenstra                                            |
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