[gmx-users] pdb2gmx and periodic molecule

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Apr 26 08:44:45 CEST 2015

Hi Alex,

I think the best way is to extend the chain, such that you get an overlap
between both ends. So for a stretch of DNA


You would generate


Then you strip off the terminal atoms and rewire the links over the
boundary. It requires renumbering the topology and at first looks a bit
cumbersome, but this ensures all the links are correct and the
modifications of the termini have no effect, and it's not very hard to
script. And, of course, scripting it is a one time effort to avoid doing it
manually later.


On Apr 26, 2015 5:55 AM, "Alex" <nedomacho at gmail.com> wrote:

> JL> The force field parameters for a phosphodiester are the same in a
> linear, finite
> JL> DNA as they will be in your infinite chain.
> I didn't mean that anything would need to be changed in the description of
> residues. The FF handles a
> finite chain perfectly.
> JL> The problem is in telling pdb2gmx
> JL> "don't link i,i+1 here, instead link i,i+(some number of intervening
> nucleotides)."
> This is exactly what I meant, the linking. Is there a way to achieve this
> without messing with the code? I just haven't looked at the code, so
> if you think I'm being a cheeky little bastard, I'll accept that. :)
> Thanks,
> Alex
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