Dear community,
I hope this isn't a duplicate but I don't know the proper
terminology for what I'd like to do. I have made a simulation box for a
single channel embedded in membrane, however, I'd like to see if the
channel can dimerize. Most other modeling programs such as AF3 are not
working for my channel for a variety of reasons. So I'd like to try a
mixture of CG and full atom MD to analyze the channel/channel interactions.
What i currently have is a 300K atom simulation box of a single channel and
I was wondering if I can tile/fuse/stitch together these boxes in a grid
(2X1/2X2/3X3?) to assess the movement of the channels. So essentially I'd
like to line up the membrane so that I have 2-4 channels in a simulation
and allow the channels to cross box boundaries, maybe by converting the
tiled boxes into a single simulation? Is this possible? the other option is
to create a protein session with 4 channels in the same membrane axis and
build a simulation in charmm-gui around that. but I'm not sure how to make
sure all the channels are in the same line and not offset in a way where
not all the channels are oriented in the membrane properly.
Any suggestions? I think this is possible in gromacs CG as I read a paper
by Dr. Anna Duncan who described this but I couldn't find a protocol for
AMBER.
Thanks everyone for your time,
Ryan
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Received on Fri Sep 20 2024 - 17:00:02 PDT
