[gmx-users] hbonds in DNA and RNA

[brynza]

Hi all,
The problem we faced dealing with RNA dynamics is quite confusing:
after fixing problems with uracil, adding of all necessary hydrogens,
etc, the RNAs we "tortured" both in vacuum and solution lost all
complementary interactions and secondary structures distorted
substantially. When we tracked all manipulations we did, we found that
pdb2gmx cannot find donors, acceptors and as a result no hbonds are
formed. For proteins everything is ok. Has anyone faced such problem?
And what parameters are responsible for hbond formation in gromacs
force field?
Thnx in advance for any helpful suggestions.
Timofei,
MSU, Chem.Dpt.

  

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Best regards,
 brynza                          mailto:brynza at mail.ru