On 10/7/13 1:39 PM, bipin singh wrote:
Thanks for the reply Dr. Justin.
I have also thinking of the same possibility but to further confirm, I am
sending the link for the plot of the distance between the COM of ligand
binding pocket and COM of ligand molecule, please find some time to have a
look at the plot and let me know if it seems a feasible behaviour during a
simulation.
http://researchweb.iiit.ac.in/~bipin.singh/plot.png
Looks like nothing more than random motion to me. Since you haven't told us
what you're doing (unrestrained MD? pulling?), it's hard to comment further.
-Justin
On Mon, Oct 7, 2013 at 8:22 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 10/7/13 10:46 AM, bipin singh wrote:
Hello All,
I have calculated the distance between the binding pocket of protein and
the ligand molecule but due to ligand diffusion out of box, I am getting
wrong distance as first it increases till 5nm and then decrease again to
around 1nm during the simulation (which is not possible).
I have fitted my trajectory with using trjconv -pbc mol -ur compact
-center
(protein) option.
I have also tried the -nojump option but getting the same results for
distances.
Please suggest how to get the real distance without the PBC effect.
It sounds like that very well could be the real distance. If the ligand
diffused out, it simply becomes part of the solvent around the protein and
can diffuse around freely.
-Justin
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University of Maryland, Baltimore
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jalem...@outerbanks.umaryland.edu | (410) 706-7441
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