hi, everyone
now i am trying to pull one complex apart, which includes two proteins.
but i met one problem, when i fixed the COM of one protein,
pulling the COM of another protein, i found the pulled protein unfolding
before pulling these two proteins apart, this is not the result i expected.
my objective is to pull these two proteins apart, in order to study the
interaction between two proteins. while the structures of these two proteins
themselves don't change too much, could you give me
some suggestions?
i have read some references about AFM pulling, i found most of the papers
are to pull a small molecule(no complicated secondary structures) from a big
biological molecules, while in my case, the reference group and the pulled
group are both complicated proteins, the interactions within the proteins and
between the proteins are similiar, therefore before pulling the interface
apart, the pulled group unfolding first. so i want to know if AFM pulling in
Gromacs can do this kind of pulling?
Thanks in advance!
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