[gmx-users] nucleic acids simulation

lpgomes at procc.fiocruz.br lpgomes at procc.fiocruz.br
Wed Jul 16 19:49:01 CEST 2003

Hello Andrey and Gromacs Users,

>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?

I´ve just finished a simulation (200ps) with crystallographic DNA dodecamer, 
and the results seem very good using OPLS and PME. Comparing to AMBER4.1 I 
found better rmsd´s. H-bonds (between bases), in my case, were stable 
through this time.
But I don´t know how to help you. I have some questions too.
Some of these problems with nucleic acid hbonds can be originated by 
the "end effect", where the ends of molecules tend to move more and 
consequently hbonds brake, but at the center residues we see stable hbonds.

>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 

Luciano P Gomes

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