[gmx-users] nucleic acids simulation

Anton Feenstra feenstra at chem.vu.nl
Thu Jul 17 09:19:01 CEST 2003

Andrey V Golovin wrote:
> Hello all,
> Finally we managed to create working topologies for DNA/RNA in all
> force fields (including problems with Uridine, impropers, *.hdb and etc).
> BUT! in all cases of dynamics simulations we observe no hydrogen
> bonds. pdb2gmx fails to find any donors and acceptors, and no hydrogen
> bonds especially between complementary bases. Still g_hbond finds some
> hbonds after the dynamics, but they mostly are formed by phosphates.
> So, here is the question:
> does anybody have reasonable simulations of nucleic acids is any of
> force fields, or know possible ways of solving our problem?
> what we consider the main clue, is that gromacs can not interpret
> input as DNA/RNA, or the parameters for hbonds in nucleic acids should
> be added manually in rtp or topology...
> also is it necessary (or possible) to specify that input molecules are
> nucleic acids?

I am no 'DNA expert', but wrote much of g_hbond, so I will speculate
on possible sources of problems. g_hbond can be rather strict in what
it considers donors and acceptors, e.g. this is tailored to the typical
atom names you encounter in proteins and SPC water. For DNA this might
be different. You can check that by looking at the output to see which
atoms were identified as donors and/or acceptors. This can be a bit of
a nuisance, since I tried to give as complete information as possible
in the output files, which sometimes went to the expense of clarity.

Secondly, there may be different equilibrium geometries for h-bonds
in DNA compared to proteins (or water), but I would actually be
surprised if this is significant since the same basic physics is

Finally, something in the simulations (forcefields) may be flawed,
but as I said, I have no experience with DNA simulations so don't
trust me on this.


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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