[gmx-users] hbonds in DNA and RNA

David van der Spoel spoel at xray.bmc.uu.se
Tue May 27 13:55:02 CEST 2003

On Tue, 2003-05-27 at 13:44, brynza wrote:
> 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?

h bonds should follow from electrostatic interactions, not by special
treatment as used to be in amber. Have you check whether the charges are

> Thnx in advance for any helpful suggestions.
> Timofei,
> MSU, Chem.Dpt.
> -- 
> Best regards,
>  brynza                          mailto:brynza at mail.ru
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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