[gmx-users] nucleic acids simulation

[Andrey V Golovin]

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?



-- 
Best regards,
 Andrey                            mailto:golovin at genebee.msu.su