[gmx-users] protein dna pulling

Erik Marklund erik.marklund at kemi.uu.se
Fri Sep 21 13:45:53 CEST 2018


Not necessarily. The COM still moves if one strand moves away. Your results however suggest that the DNA’s interaction with the protein is stronger than the interaction between strands. I will leave it up to you to decide whether that makes sense or not, or if there is something wrong with your setup.

Kind regards,
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4542
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 27 Aug 2018, at 20:11, abhisek Mondal <abhisek.mndl at gmail.com<mailto:abhisek.mndl at gmail.com>> wrote:

I have been trying to pull a double stranded DNA from protein's binding
surface. But I am facing an issue. After defining the pull vector when I
apply the pull force the DNA's one stand got pulled completely while other
strand partially remain attached (
Shouldn't the both strands be moving together (as the COM was determined
using residues from both strand of DNA) ?
Some suggestions in this regard would be highly appreciated.
Thank you.

Abhisek Mondal

*Senior Research Fellow*
*Protein Crystallography Group*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

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