[gmx-users] Problem to build an infinite DNA chain ...

[Sergio Garay]

Hi all

I'm trying to build an infinite single DNA chain (all-atom AMBER bsc1 FF),
following a couple of old mails about this topic:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096970.html

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106130.html

But I have not achieved using pdb2gmx tool. I prepared my DNA with an extra
phosphate at the 5' terminal (As if this residue were inside the chain).
The number and order of the atoms is the same as the topology. Finally I
commented out all the entrance in dna.r2b file to force pdb2gmx to not make
any replacement at the terminal residues. But it still complains about the
terminals:


*Fatal error:There is a dangling bond at at least one of the terminal ends
and the force field does not provide terminal entries or files. Fix your
terminal residues so that they match the residue database (.rtp) entries,
or provide terminal database entries (.tdb).*

But there isn't any dangling bond in my molecule: the atoms in my pdb file
match perfectly with the ones in the dna.rtp file.

Can anyone give me a good clue to manage this problem? Is it possible? I
did not find any DNA simulation which treats DNA as a periodic molecule (or
may be, some of you can give any cite obout this kind of problems).

Thank you very much in advance!
Sergio