[gmx-users] kind of contacts in protein-dna interaction during simulation

Mark Abraham Mark.Abraham at anu.edu.au
Sun Nov 7 11:25:23 CET 2010

On 7/11/2010 8:02 PM, leila karami wrote:
> Hi gromacs users
> In following article, in table 2, author brings Protein–DNA contacts 
> observed in the simulation.
> I want to know how to obtain 1) Van der Waals interactions 2) 
> percentage of population regarding Direct hydrogen bond, Van der Waals 
> and Water-mediated hydrogen bond. In method section, Protein and DNA 
> atoms were considered hydrogen-bonded if the distance between hydrogen 
> and acceptor atoms was less than 2.6 A and the donor–hydrogen–acceptor 
> angle was greater than 120. Hydrophobic interaction was defined when 
> the distance between a pair of carbon atoms was less than 4 A 
> Interfacial hydration water molecules were identified by applying a 
> cut-off 2.6 A for the distance of water to protein and DNA atoms 
> simultaneously.

Take a look at section 7.4 of the manual, where it groups the tools by 
analysis type, and use that to see which tools might be useful.


> J. Mol. Recognit. 2004; 17: 120–131
> DOI:10.1002/jmr.658
> The role of flexibility and hydration on the sequence-specific DNA 
> recognition by the Tn916 integrase protein: a molecular dynamics 
> analysis.
> -- 
> Leila Karami
> Ph.D. student of Physical Chemistry
> K.N. Toosi University of Technology
> Theoretical Physical Chemistry Group

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