[gmx-users] protein dna pulling

[Erik Marklund]

Hi,

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
______________________________________________
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:

Hi,
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 (
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
).
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*

*INDIA*
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